Skip to content

GitLab

C
cornet
Commit 7a51fb57 authored by Armin Rauschenberger's avatar Armin Rauschenberger
Browse files
Options

remove file

parent fd42b873
Expand all Hide whitespace changes
Inline Side-by-side
Showing with 1061 additions and 674 deletions
DESCRIPTION
View file @ 7a51fb57
...@@ -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: 6.1.1 RoxygenNote: 7.1.1
URL: https://github.com/rauschenberger/cornet URL: https://github.com/rauschenberger/cornet
BugReports: https://github.com/rauschenberger/cornet/issues BugReports: https://github.com/rauschenberger/cornet/issues
cran-comments.md
View file @ 7a51fb57
# Notes # Notes
- reason for resubmission: updated documentation
\ No newline at end of file
docs/404.html
View file @ 7a51fb57
...@@ -10,23 +10,27 @@ ...@@ -10,23 +10,27 @@
<!-- jquery --> <!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap --> <!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" /> <link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
<!-- bootstrap-toc -->
<link rel="stylesheet" href="bootstrap-toc.css">
<script src="bootstrap-toc.js"></script>
<!-- Font Awesome icons --> <!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
<!-- clipboard.js --> <!-- 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> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
<!-- headroom.js --> <!-- headroom.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown --> <!-- pkgdown -->
<link href="pkgdown.css" rel="stylesheet"> <link href="pkgdown.css" rel="stylesheet">
...@@ -53,7 +57,7 @@ ...@@ -53,7 +57,7 @@
</head> </head>
<body> <body data-spy="scroll" data-target="#toc">
<div class="container template-title-body"> <div class="container template-title-body">
<header> <header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="navbar navbar-default navbar-fixed-top" role="navigation">
...@@ -125,6 +129,12 @@ Content not found. Please use links in the navbar. ...@@ -125,6 +129,12 @@ Content not found. Please use links in the navbar.
</div> </div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div> </div>
...@@ -135,7 +145,7 @@ Content not found. Please use links in the navbar. ...@@ -135,7 +145,7 @@ Content not found. Please use links in the navbar.
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div> </div>
</footer> </footer>
......
docs/articles/application.html
View file @ 7a51fb57
This diff is collapsed.
docs/articles/article.html
View file @ 7a51fb57
...@@ -6,19 +6,19 @@ ...@@ -6,19 +6,19 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Lasso and ridge regression for dichotomised outcomes • cornet</title> <title>Lasso and ridge regression for dichotomised outcomes • cornet</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><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> <!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous"> <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous"> <script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
<!-- 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><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
<script src="../pkgdown.js"></script><meta property="og:title" content="Lasso and ridge regression for dichotomised outcomes"> <script src="../pkgdown.js"></script><meta property="og:title" content="Lasso and ridge regression for dichotomised outcomes">
<meta property="og:description" content=""> <meta property="og:description" content="cornet">
<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]> <!-- 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/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]--> <![endif]-->
</head> </head>
<body> <body data-spy="scroll" data-target="#toc">
<div class="container template-article"> <div class="container template-article">
<header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container"> <div class="container">
...@@ -82,7 +82,7 @@ ...@@ -82,7 +82,7 @@
</header><div class="row"> </header><div class="row">
<div class="col-md-9 contents"> <div class="col-md-9 contents">
<div class="page-header toc-ignore"> <div class="page-header toc-ignore">
<h1>Lasso and ridge regression for dichotomised outcomes</h1> <h1 data-toc-skip>Lasso and ridge regression for dichotomised outcomes</h1>
<small class="dont-index">Source: <a href="https://github.com/rauschenberger/cornet/blob/master/vignettes/article.Rmd"><code>vignettes/article.Rmd</code></a></small> <small class="dont-index">Source: <a href="https://github.com/rauschenberger/cornet/blob/master/vignettes/article.Rmd"><code>vignettes/article.Rmd</code></a></small>
...@@ -100,16 +100,11 @@ ...@@ -100,16 +100,11 @@
</div> </div>
</div> </div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<div id="tocnav"> <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2>
<h2 class="hasAnchor"> </nav>
<a href="#tocnav" class="anchor"></a>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#reference">Reference</a></li>
</ul>
</div> </div>
</div>
</div> </div>
...@@ -120,7 +115,7 @@ ...@@ -120,7 +115,7 @@
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div> </div>
</footer> </footer>
......
docs/articles/index.html
View file @ 7a51fb57
...@@ -10,23 +10,27 @@ ...@@ -10,23 +10,27 @@
<!-- jquery --> <!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap --> <!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" /> <link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
<!-- Font Awesome icons --> <!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
<!-- clipboard.js --> <!-- 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> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
<!-- headroom.js --> <!-- headroom.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown --> <!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet"> <link href="../pkgdown.css" rel="stylesheet">
...@@ -53,7 +57,7 @@ ...@@ -53,7 +57,7 @@
</head> </head>
<body> <body data-spy="scroll" data-target="#toc">
<div class="container template-article-index"> <div class="container template-article-index">
<header> <header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="navbar navbar-default navbar-fixed-top" role="navigation">
...@@ -125,12 +129,16 @@ ...@@ -125,12 +129,16 @@
<h3>All vignettes</h3> <h3>All vignettes</h3>
<p class="section-desc"></p> <p class="section-desc"></p>
<ul> <dl>
<li><a href="application.html">reproducibility - application</a></li> <dt><a href="application.html">reproducibility - application</a></dt>
<li><a href="article.html">Lasso and ridge regression for dichotomised outcomes</a></li> <dd></dt>
<li><a href="simulation.html">reproducibility - simulation</a></li> <dt><a href="article.html">Lasso and ridge regression for dichotomised outcomes</a></dt>
<li><a href="vignette.html">Combined Regression</a></li> <dd></dt>
</ul> <dt><a href="simulation.html">reproducibility - simulation</a></dt>
<dd></dt>
<dt><a href="vignette.html">Combined Regression</a></dt>
<dd></dt>
</dl>
</div> </div>
</div> </div>
</div> </div>
...@@ -142,7 +150,7 @@ ...@@ -142,7 +150,7 @@
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div> </div>
</footer> </footer>
......
docs/articles/simulation.html
View file @ 7a51fb57
This diff is collapsed.
docs/articles/vignette.html
View file @ 7a51fb57
This diff is collapsed.
docs/authors.html
View file @ 7a51fb57
...@@ -10,23 +10,27 @@ ...@@ -10,23 +10,27 @@
<!-- jquery --> <!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap --> <!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" /> <link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
<!-- bootstrap-toc -->
<link rel="stylesheet" href="bootstrap-toc.css">
<script src="bootstrap-toc.js"></script>
<!-- Font Awesome icons --> <!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
<!-- clipboard.js --> <!-- 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> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
<!-- headroom.js --> <!-- headroom.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown --> <!-- pkgdown -->
<link href="pkgdown.css" rel="stylesheet"> <link href="pkgdown.css" rel="stylesheet">
...@@ -53,7 +57,7 @@ ...@@ -53,7 +57,7 @@
</head> </head>
<body> <body data-spy="scroll" data-target="#toc">
<div class="container template-authors"> <div class="container template-authors">
<header> <header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="navbar navbar-default navbar-fixed-top" role="navigation">
...@@ -140,7 +144,7 @@ ...@@ -140,7 +144,7 @@
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div> </div>
</footer> </footer>
......
docs/bootstrap-toc.css 0 → 100644
View file @ 7a51fb57
/*!
* Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/)
* Copyright 2015 Aidan Feldman
* Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */
/* modified from https://github.com/twbs/bootstrap/blob/94b4076dd2efba9af71f0b18d4ee4b163aa9e0dd/docs/assets/css/src/docs.css#L548-L601 */
/* All levels of nav */
nav[data-toggle='toc'] .nav > li > a {
display: block;
padding: 4px 20px;
font-size: 13px;
font-weight: 500;
color: #767676;
}
nav[data-toggle='toc'] .nav > li > a:hover,
nav[data-toggle='toc'] .nav > li > a:focus {
padding-left: 19px;
color: #563d7c;
text-decoration: none;
background-color: transparent;
border-left: 1px solid #563d7c;
}
nav[data-toggle='toc'] .nav > .active > a,
nav[data-toggle='toc'] .nav > .active:hover > a,
nav[data-toggle='toc'] .nav > .active:focus > a {
padding-left: 18px;
font-weight: bold;
color: #563d7c;
background-color: transparent;
border-left: 2px solid #563d7c;
}
/* Nav: second level (shown on .active) */
nav[data-toggle='toc'] .nav .nav {
display: none; /* Hide by default, but at >768px, show it */
padding-bottom: 10px;
}
nav[data-toggle='toc'] .nav .nav > li > a {
padding-top: 1px;
padding-bottom: 1px;
padding-left: 30px;
font-size: 12px;
font-weight: normal;
}
nav[data-toggle='toc'] .nav .nav > li > a:hover,
nav[data-toggle='toc'] .nav .nav > li > a:focus {
padding-left: 29px;
}
nav[data-toggle='toc'] .nav .nav > .active > a,
nav[data-toggle='toc'] .nav .nav > .active:hover > a,
nav[data-toggle='toc'] .nav .nav > .active:focus > a {
padding-left: 28px;
font-weight: 500;
}
/* from https://github.com/twbs/bootstrap/blob/e38f066d8c203c3e032da0ff23cd2d6098ee2dd6/docs/assets/css/src/docs.css#L631-L634 */
nav[data-toggle='toc'] .nav > .active > ul {
display: block;
}
docs/bootstrap-toc.js 0 → 100644
View file @ 7a51fb57
/*!
* Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/)
* Copyright 2015 Aidan Feldman
* Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */
(function() {
'use strict';
window.Toc = {
helpers: {
// return all matching elements in the set, or their descendants
findOrFilter: function($el, selector) {
// http://danielnouri.org/notes/2011/03/14/a-jquery-find-that-also-finds-the-root-element/
// http://stackoverflow.com/a/12731439/358804
var $descendants = $el.find(selector);
return $el.filter(selector).add($descendants).filter(':not([data-toc-skip])');
},
generateUniqueIdBase: function(el) {
var text = $(el).text();
var anchor = text.trim().toLowerCase().replace(/[^A-Za-z0-9]+/g, '-');
return anchor || el.tagName.toLowerCase();
},
generateUniqueId: function(el) {
var anchorBase = this.generateUniqueIdBase(el);
for (var i = 0; ; i++) {
var anchor = anchorBase;
if (i > 0) {
// add suffix
anchor += '-' + i;
}
// check if ID already exists
if (!document.getElementById(anchor)) {
return anchor;
}
}
},
generateAnchor: function(el) {
if (el.id) {
return el.id;
} else {
var anchor = this.generateUniqueId(el);
el.id = anchor;
return anchor;
}
},
createNavList: function() {
return $('<ul class="nav"></ul>');
},
createChildNavList: function($parent) {
var $childList = this.createNavList();
$parent.append($childList);
return $childList;
},
generateNavEl: function(anchor, text) {
var $a = $('<a></a>');
$a.attr('href', '#' + anchor);
$a.text(text);
var $li = $('<li></li>');
$li.append($a);
return $li;
},
generateNavItem: function(headingEl) {
var anchor = this.generateAnchor(headingEl);
var $heading = $(headingEl);
var text = $heading.data('toc-text') || $heading.text();
return this.generateNavEl(anchor, text);
},
// Find the first heading level (`<h1>`, then `<h2>`, etc.) that has more than one element. Defaults to 1 (for `<h1>`).
getTopLevel: function($scope) {
for (var i = 1; i <= 6; i++) {
var $headings = this.findOrFilter($scope, 'h' + i);
if ($headings.length > 1) {
return i;
}
}
return 1;
},
// returns the elements for the top level, and the next below it
getHeadings: function($scope, topLevel) {
var topSelector = 'h' + topLevel;
var secondaryLevel = topLevel + 1;
var secondarySelector = 'h' + secondaryLevel;
return this.findOrFilter($scope, topSelector + ',' + secondarySelector);
},
getNavLevel: function(el) {
return parseInt(el.tagName.charAt(1), 10);
},
populateNav: function($topContext, topLevel, $headings) {
var $context = $topContext;
var $prevNav;
var helpers = this;
$headings.each(function(i, el) {
var $newNav = helpers.generateNavItem(el);
var navLevel = helpers.getNavLevel(el);
// determine the proper $context
if (navLevel === topLevel) {
// use top level
$context = $topContext;
} else if ($prevNav && $context === $topContext) {
// create a new level of the tree and switch to it
$context = helpers.createChildNavList($prevNav);
} // else use the current $context
$context.append($newNav);
$prevNav = $newNav;
});
},
parseOps: function(arg) {
var opts;
if (arg.jquery) {
opts = {
$nav: arg
};
} else {
opts = arg;
}
opts.$scope = opts.$scope || $(document.body);
return opts;
}
},
// accepts a jQuery object, or an options object
init: function(opts) {
opts = this.helpers.parseOps(opts);
// ensure that the data attribute is in place for styling
opts.$nav.attr('data-toggle', 'toc');
var $topContext = this.helpers.createChildNavList(opts.$nav);
var topLevel = this.helpers.getTopLevel(opts.$scope);
var $headings = this.helpers.getHeadings(opts.$scope, topLevel);
this.helpers.populateNav($topContext, topLevel, $headings);
}
};
$(function() {
$('nav[data-toggle="toc"]').each(function(i, el) {
var $nav = $(el);
Toc.init($nav);
});
});
})();
docs/index.html
View file @ 7a51fb57
...@@ -6,19 +6,19 @@ ...@@ -6,19 +6,19 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Elastic Net with Dichotomised Outcomes • cornet</title> <title>Elastic Net with Dichotomised Outcomes • cornet</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><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> <!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous"> <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="bootstrap-toc.css">
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous"> <script src="bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
<!-- 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><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
<script src="pkgdown.js"></script><meta property="og:title" content="Elastic Net with Dichotomised Outcomes"> <script src="pkgdown.js"></script><meta property="og:title" content="Elastic Net with Dichotomised Outcomes">
<meta property="og:description" content="Implements lasso and ridge regression for dichotomised outcomes (Rauschenberger et al. 2019). Such outcomes are not naturally but artificially binary. They indicate whether an underlying measurement is greater than a threshold."> <meta property="og:description" content="Implements lasso and ridge regression for dichotomised outcomes (Rauschenberger et al. 2019). Such outcomes are not naturally but artificially binary. They indicate whether an underlying measurement is greater than a threshold.">
<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]> <!-- 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/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]--> <![endif]-->
</head> </head>
<body> <body data-spy="scroll" data-target="#toc">
<div class="container template-home"> <div class="container template-home">
<header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container"> <div class="container">
...@@ -92,10 +92,10 @@ ...@@ -92,10 +92,10 @@
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#installation" class="anchor"></a>Installation</h2> <a href="#installation" class="anchor"></a>Installation</h2>
<p>Install the current release from <a href="https://CRAN.R-project.org/package=cornet">CRAN</a>:</p> <p>Install the current release from <a href="https://CRAN.R-project.org/package=cornet">CRAN</a>:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"cornet"</span>)</a></code></pre></div> <div class="sourceCode" id="cb1"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"cornet"</span>)</pre></div>
<p>or the latest development version from <a href="https://github.com/rauschenberger/cornet">GitHub</a>:</p> <p>or the latest development version from <a href="https://github.com/rauschenberger/cornet">GitHub</a>:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1"><span class="co">#install.packages("devtools")</span></a> <div class="sourceCode" id="cb2"><pre class="r"><span class="co">#install.packages("devtools")</span>
<a class="sourceLine" id="cb2-2" title="2">devtools<span class="op">::</span><span class="kw"><a href="https://rdrr.io/pkg/devtools/man/remote-reexports.html">install_github</a></span>(<span class="st">"rauschenberger/cornet"</span>)</a></code></pre></div> <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/cornet"</span>)</pre></div>
</div> </div>
<div id="reference" class="section level2"> <div id="reference" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
...@@ -106,13 +106,13 @@ ...@@ -106,13 +106,13 @@
</div> </div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<div class="links"> <div class="links">
<h2>Links</h2> <h2>Links</h2>
<ul class="list-unstyled"> <ul class="list-unstyled">
<li>Download from CRAN at <br><a href="https://cloud.r-project.org/package=cornet">https://​cloud.r-project.org/​package=cornet</a> <li>Download from CRAN at <br><a href="https://cloud.r-project.org/package=cornet">https://​cloud.r-project.org/​package=cornet</a>
</li> </li>
<li>Browse source code at <br><a href="https://github.com/rauschenberger/cornet">https://​github.com/​rauschenberger/​cornet</a> <li>Browse source code at <br><a href="https://github.com/rauschenberger/cornet/">https://​github.com/​rauschenberger/​cornet/​</a>
</li> </li>
<li>Report a bug at <br><a href="https://github.com/rauschenberger/cornet/issues">https://​github.com/​rauschenberger/​cornet/​issues</a> <li>Report a bug at <br><a href="https://github.com/rauschenberger/cornet/issues">https://​github.com/​rauschenberger/​cornet/​issues</a>
</li> </li>
...@@ -151,7 +151,7 @@ ...@@ -151,7 +151,7 @@
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div> </div>
</footer> </footer>
......
docs/news/index.html
View file @ 7a51fb57
...@@ -10,23 +10,27 @@ ...@@ -10,23 +10,27 @@
<!-- jquery --> <!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap --> <!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" /> <link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
<!-- Font Awesome icons --> <!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
<!-- clipboard.js --> <!-- 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> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
<!-- headroom.js --> <!-- headroom.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown --> <!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet"> <link href="../pkgdown.css" rel="stylesheet">
...@@ -53,7 +57,7 @@ ...@@ -53,7 +57,7 @@
</head> </head>
<body> <body data-spy="scroll" data-target="#toc">
<div class="container template-news"> <div class="container template-news">
<header> <header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="navbar navbar-default navbar-fixed-top" role="navigation">
...@@ -118,7 +122,7 @@ ...@@ -118,7 +122,7 @@
<div class="row"> <div class="row">
<div class="col-md-9 contents"> <div class="col-md-9 contents">
<div class="page-header"> <div class="page-header">
<h1>Changelog <small></small></h1> <h1 data-toc-skip>Changelog <small></small></h1>
<small>Source: <a href='https://github.com/rauschenberger/cornet/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/rauschenberger/cornet/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
...@@ -161,17 +165,10 @@ ...@@ -161,17 +165,10 @@
</div> </div>
</div> </div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<div id="tocnav"> <nav id="toc" data-toggle="toc" class="sticky-top">
<h2>Contents</h2> <h2 data-toc-skip>Contents</h2>
<ul class="nav nav-pills nav-stacked"> </nav>
<li><a href="#cornet-004-2020-03-18">0.0.4</a></li>
<li><a href="#cornet-003-2019-11-12">0.0.3</a></li>
<li><a href="#cornet-003-2019-10-02">0.0.3</a></li>
<li><a href="#cornet-002-2019-09-26">0.0.2</a></li>
<li><a href="#cornet-001-2019-03-21">0.0.1</a></li>
</ul>
</div>
</div> </div>
</div> </div>
...@@ -183,7 +180,7 @@ ...@@ -183,7 +180,7 @@
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div> </div>
</footer> </footer>
......
docs/pkgdown.css
View file @ 7a51fb57
...@@ -17,6 +17,10 @@ html, body { ...@@ -17,6 +17,10 @@ html, body {
height: 100%; height: 100%;
} }
body {
position: relative;
}
body > .container { body > .container {
display: flex; display: flex;
height: 100%; height: 100%;
...@@ -67,6 +71,10 @@ summary { ...@@ -67,6 +71,10 @@ summary {
margin-top: calc(-60px + 1em); margin-top: calc(-60px + 1em);
} }
dd {
margin-left: 3em;
}
/* Section anchors ---------------------------------*/ /* Section anchors ---------------------------------*/
a.anchor { a.anchor {
...@@ -100,29 +108,132 @@ a.anchor { ...@@ -100,29 +108,132 @@ a.anchor {
margin-top: -40px; margin-top: -40px;
} }
/* Navbar submenu --------------------------*/
.dropdown-submenu {
position: relative;
}
.dropdown-submenu>.dropdown-menu {
top: 0;
left: 100%;
margin-top: -6px;
margin-left: -1px;
border-radius: 0 6px 6px 6px;
}
.dropdown-submenu:hover>.dropdown-menu {
display: block;
}
.dropdown-submenu>a:after {
display: block;
content: " ";
float: right;
width: 0;
height: 0;
border-color: transparent;
border-style: solid;
border-width: 5px 0 5px 5px;
border-left-color: #cccccc;
margin-top: 5px;
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #ffffff;
}
.dropdown-submenu.pull-left {
float: none;
}
.dropdown-submenu.pull-left>.dropdown-menu {
left: -100%;
margin-left: 10px;
border-radius: 6px 0 6px 6px;
}
/* Sidebar --------------------------*/ /* Sidebar --------------------------*/
#sidebar { #pkgdown-sidebar {
margin-top: 30px; margin-top: 30px;
position: -webkit-sticky; position: -webkit-sticky;
position: sticky; position: sticky;
top: 70px; top: 70px;
} }
#sidebar h2 {
#pkgdown-sidebar h2 {
font-size: 1.5em; font-size: 1.5em;
margin-top: 1em; margin-top: 1em;
} }
#sidebar h2:first-child { #pkgdown-sidebar h2:first-child {
margin-top: 0; margin-top: 0;
} }
#sidebar .list-unstyled li { #pkgdown-sidebar .list-unstyled li {
margin-bottom: 0.5em; margin-bottom: 0.5em;
} }
/* bootstrap-toc tweaks ------------------------------------------------------*/
/* All levels of nav */
nav[data-toggle='toc'] .nav > li > a {
padding: 4px 20px 4px 6px;
font-size: 1.5rem;
font-weight: 400;
color: inherit;
}
nav[data-toggle='toc'] .nav > li > a:hover,
nav[data-toggle='toc'] .nav > li > a:focus {
padding-left: 5px;
color: inherit;
border-left: 1px solid #878787;
}
nav[data-toggle='toc'] .nav > .active > a,
nav[data-toggle='toc'] .nav > .active:hover > a,
nav[data-toggle='toc'] .nav > .active:focus > a {
padding-left: 5px;
font-size: 1.5rem;
font-weight: 400;
color: inherit;
border-left: 2px solid #878787;
}
/* Nav: second level (shown on .active) */
nav[data-toggle='toc'] .nav .nav {
display: none; /* Hide by default, but at >768px, show it */
padding-bottom: 10px;
}
nav[data-toggle='toc'] .nav .nav > li > a {
padding-left: 16px;
font-size: 1.35rem;
}
nav[data-toggle='toc'] .nav .nav > li > a:hover,
nav[data-toggle='toc'] .nav .nav > li > a:focus {
padding-left: 15px;
}
nav[data-toggle='toc'] .nav .nav > .active > a,
nav[data-toggle='toc'] .nav .nav > .active:hover > a,
nav[data-toggle='toc'] .nav .nav > .active:focus > a {
padding-left: 15px;
font-weight: 500;
font-size: 1.35rem;
}
/* orcid ------------------------------------------------------------------- */
.orcid { .orcid {
height: 16px; font-size: 16px;
color: #A6CE39;
/* margins are required by official ORCID trademark and display guidelines */ /* margins are required by official ORCID trademark and display guidelines */
margin-left:4px; margin-left:4px;
margin-right:4px; margin-right:4px;
......
docs/pkgdown.js
View file @ 7a51fb57
...@@ -9,11 +9,6 @@ ...@@ -9,11 +9,6 @@
$('body').css('padding-top', $('.navbar').height() + 10); $('body').css('padding-top', $('.navbar').height() + 10);
}); });
$('body').scrollspy({
target: '#sidebar',
offset: 60
});
$('[data-toggle="tooltip"]').tooltip(); $('[data-toggle="tooltip"]').tooltip();
var cur_path = paths(location.pathname); var cur_path = paths(location.pathname);
......
docs/pkgdown.yml
View file @ 7a51fb57
pandoc: 2.7.2 pandoc: 2.7.2
pkgdown: 1.4.1 pkgdown: 1.5.1
pkgdown_sha: ~ pkgdown_sha: ~
articles: articles:
application: application.html application: application.html
article: article.html article: article.html
simulation: simulation.html simulation: simulation.html
vignette: vignette.html vignette: vignette.html
last_built: 2020-09-07T10:17Z
docs/reference/coef.cornet.html
View file @ 7a51fb57
...@@ -10,23 +10,27 @@ ...@@ -10,23 +10,27 @@
<!-- jquery --> <!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap --> <!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" /> <link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
<!-- Font Awesome icons --> <!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
<!-- clipboard.js --> <!-- 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> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
<!-- headroom.js --> <!-- headroom.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown --> <!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet"> <link href="../pkgdown.css" rel="stylesheet">
...@@ -38,7 +42,6 @@ ...@@ -38,7 +42,6 @@
<meta property="og:title" content="Extract estimated coefficients — coef.cornet" /> <meta property="og:title" content="Extract estimated coefficients — coef.cornet" />
<meta property="og:description" content="Extracts estimated coefficients from linear and logistic regression, <meta property="og:description" content="Extracts estimated coefficients from linear and logistic regression,
under the penalty parameter that minimises the cross-validated loss." /> under the penalty parameter that minimises the cross-validated loss." />
<meta name="twitter:card" content="summary" />
...@@ -56,7 +59,7 @@ under the penalty parameter that minimises the cross-validated loss." /> ...@@ -56,7 +59,7 @@ under the penalty parameter that minimises the cross-validated loss." />
</head> </head>
<body> <body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic"> <div class="container template-reference-topic">
<header> <header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="navbar navbar-default navbar-fixed-top" role="navigation">
...@@ -363,14 +366,10 @@ and logistic regression (2nd column: <code>"gamma"</code>).</p> ...@@ -363,14 +366,10 @@ and logistic regression (2nd column: <code>"gamma"</code>).</p>
#&gt; V200 . -0.0640594</div><div class='input'> #&gt; V200 . -0.0640594</div><div class='input'>
</div></pre> </div></pre>
</div> </div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2> <nav id="toc" data-toggle="toc" class="sticky-top">
<ul class="nav nav-pills nav-stacked"> <h2 data-toc-skip>Contents</h2>
<li><a href="#arguments">Arguments</a></li> </nav>
<li><a href="#value">Value</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
</div> </div>
</div> </div>
...@@ -381,7 +380,7 @@ and logistic regression (2nd column: <code>"gamma"</code>).</p> ...@@ -381,7 +380,7 @@ and logistic regression (2nd column: <code>"gamma"</code>).</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div> </div>
</footer> </footer>
......
docs/reference/cornet.html
View file @ 7a51fb57
...@@ -10,23 +10,27 @@ ...@@ -10,23 +10,27 @@
<!-- jquery --> <!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap --> <!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" /> <link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
<!-- Font Awesome icons --> <!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
<!-- clipboard.js --> <!-- 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> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
<!-- headroom.js --> <!-- headroom.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown --> <!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet"> <link href="../pkgdown.css" rel="stylesheet">
...@@ -39,7 +43,6 @@ ...@@ -39,7 +43,6 @@
<meta property="og:description" content="Implements lasso and ridge regression for dichotomised outcomes. <meta property="og:description" content="Implements lasso and ridge regression for dichotomised outcomes.
Such outcomes are not naturally but artificially binary. Such outcomes are not naturally but artificially binary.
They indicate whether an underlying measurement is greater than a threshold." /> They indicate whether an underlying measurement is greater than a threshold." />
<meta name="twitter:card" content="summary" />
...@@ -57,7 +60,7 @@ They indicate whether an underlying measurement is greater than a threshold." /> ...@@ -57,7 +60,7 @@ They indicate whether an underlying measurement is greater than a threshold." />
</head> </head>
<body> <body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic"> <div class="container template-reference-topic">
<header> <header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="navbar navbar-default navbar-fixed-top" role="navigation">
...@@ -133,9 +136,20 @@ Such outcomes are not naturally but artificially binary. ...@@ -133,9 +136,20 @@ Such outcomes are not naturally but artificially binary.
They indicate whether an underlying measurement is greater than a threshold.</p> They indicate whether an underlying measurement is greater than a threshold.</p>
</div> </div>
<pre class="usage"><span class='fu'>cornet</span>(<span class='no'>y</span>, <span class='no'>cutoff</span>, <span class='no'>X</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>1</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>, <pre class="usage"><span class='fu'>cornet</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='no'>y</span>,
<span class='kw'>type.measure</span> <span class='kw'>=</span> <span class='st'>"deviance"</span>, <span class='no'>...</span>)</pre> <span class='no'>cutoff</span>,
<span class='no'>X</span>,
<span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>1</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'>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'>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">
...@@ -255,17 +269,10 @@ If at all, use <code>"auc"</code> for external cross-validation only.</p> ...@@ -255,17 +269,10 @@ If at all, use <code>"auc"</code> for external cross-validation only.</p>
#&gt; deviance = 1.3</div><div class='input'> #&gt; deviance = 1.3</div><div class='input'>
</div></pre> </div></pre>
</div> </div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2> <nav id="toc" data-toggle="toc" class="sticky-top">
<ul class="nav nav-pills nav-stacked"> <h2 data-toc-skip>Contents</h2>
<li><a href="#arguments">Arguments</a></li> </nav>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#references">References</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
</div> </div>
</div> </div>
...@@ -276,7 +283,7 @@ If at all, use <code>"auc"</code> for external cross-validation only.</p> ...@@ -276,7 +283,7 @@ If at all, use <code>"auc"</code> for external cross-validation only.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div> </div>
</footer> </footer>
......
docs/reference/cv.cornet.html
View file @ 7a51fb57
...@@ -10,23 +10,27 @@ ...@@ -10,23 +10,27 @@
<!-- jquery --> <!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap --> <!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" /> <link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
<!-- Font Awesome icons --> <!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
<!-- clipboard.js --> <!-- 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> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
<!-- headroom.js --> <!-- headroom.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown --> <!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet"> <link href="../pkgdown.css" rel="stylesheet">
...@@ -37,7 +41,6 @@ ...@@ -37,7 +41,6 @@
<meta property="og:title" content="Performance measurement — cv.cornet" /> <meta property="og:title" content="Performance measurement — cv.cornet" />
<meta property="og:description" content="Compares models for a continuous response with a cut-off value." /> <meta property="og:description" content="Compares models for a continuous response with a cut-off value." />
<meta name="twitter:card" content="summary" />
...@@ -55,7 +58,7 @@ ...@@ -55,7 +58,7 @@
</head> </head>
<body> <body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic"> <div class="container template-reference-topic">
<header> <header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="navbar navbar-default navbar-fixed-top" role="navigation">
...@@ -129,9 +132,18 @@ ...@@ -129,9 +132,18 @@
<p>Compares models for a continuous response with a cut-off value.</p> <p>Compares models for a continuous response with a cut-off value.</p>
</div> </div>
<pre class="usage"><span class='fu'>cv.cornet</span>(<span class='no'>y</span>, <span class='no'>cutoff</span>, <span class='no'>X</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>nfolds.ext</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>nfolds.int</span> <span class='kw'>=</span> <span class='fl'>10</span>, <pre class="usage"><span class='fu'>cv.cornet</span>(
<span class='kw'>foldid.ext</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>foldid.int</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='no'>y</span>,
<span class='no'>...</span>)</pre> <span class='no'>cutoff</span>,
<span class='no'>X</span>,
<span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>1</span>,
<span class='kw'>nfolds.ext</span> <span class='kw'>=</span> <span class='fl'>5</span>,
<span class='kw'>nfolds.int</span> <span class='kw'>=</span> <span class='fl'>10</span>,
<span class='kw'>foldid.ext</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>foldid.int</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='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">
...@@ -206,14 +218,10 @@ or <code>"class"</code> (see <code><a href='https://rdrr.io/pkg/glmnet/man/cv.gl ...@@ -206,14 +218,10 @@ or <code>"class"</code> (see <code><a href='https://rdrr.io/pkg/glmnet/man/cv.gl
<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='no'>n</span>)</div><div class='output co'>#&gt; <span class='error'>Error in rnorm(n): object 'n' not found</span></div><div class='input'><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>)</div><div class='output co'>#&gt; <span class='error'>Error in rnorm(n * p): object 'n' not found</span></div><div class='input'><span class='no'>loss</span> <span class='kw'>&lt;-</span> <span class='fu'>cv.cornet</span>(<span class='kw'>y</span><span class='kw'>=</span><span class='no'>y</span>,<span class='kw'>cutoff</span><span class='kw'>=</span><span class='fl'>0</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 cv.cornet(y = y, cutoff = 0, X = X): object 'y' not found</span></div><div class='input'><span class='no'>loss</span></div><div class='output co'>#&gt; <span class='error'>Error in eval(expr, envir, enclos): object 'loss' not found</span></div><div class='input'> <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='no'>n</span>)</div><div class='output co'>#&gt; <span class='error'>Error in rnorm(n): object 'n' not found</span></div><div class='input'><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>)</div><div class='output co'>#&gt; <span class='error'>Error in rnorm(n * p): object 'n' not found</span></div><div class='input'><span class='no'>loss</span> <span class='kw'>&lt;-</span> <span class='fu'>cv.cornet</span>(<span class='kw'>y</span><span class='kw'>=</span><span class='no'>y</span>,<span class='kw'>cutoff</span><span class='kw'>=</span><span class='fl'>0</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 cv.cornet(y = y, cutoff = 0, X = X): object 'y' not found</span></div><div class='input'><span class='no'>loss</span></div><div class='output co'>#&gt; <span class='error'>Error in eval(expr, envir, enclos): object 'loss' not found</span></div><div class='input'>
</div></pre> </div></pre>
</div> </div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2> <nav id="toc" data-toggle="toc" class="sticky-top">
<ul class="nav nav-pills nav-stacked"> <h2 data-toc-skip>Contents</h2>
<li><a href="#arguments">Arguments</a></li> </nav>
<li><a href="#details">Details</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
</div> </div>
</div> </div>
...@@ -224,7 +232,7 @@ or <code>"class"</code> (see <code><a href='https://rdrr.io/pkg/glmnet/man/cv.gl ...@@ -224,7 +232,7 @@ or <code>"class"</code> (see <code><a href='https://rdrr.io/pkg/glmnet/man/cv.gl
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div> </div>
</footer> </footer>
......
docs/reference/dot-check.html
View file @ 7a51fb57
...@@ -10,23 +10,27 @@ ...@@ -10,23 +10,27 @@
<!-- jquery --> <!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap --> <!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" /> <link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
<!-- Font Awesome icons --> <!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
<!-- clipboard.js --> <!-- 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> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
<!-- headroom.js --> <!-- headroom.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown --> <!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet"> <link href="../pkgdown.css" rel="stylesheet">
...@@ -37,7 +41,6 @@ ...@@ -37,7 +41,6 @@
<meta property="og:title" content="Arguments — .check" /> <meta property="og:title" content="Arguments — .check" />
<meta property="og:description" content="Verifies whether an argument matches formal requirements." /> <meta property="og:description" content="Verifies whether an argument matches formal requirements." />
<meta name="twitter:card" content="summary" />
...@@ -55,7 +58,7 @@ ...@@ -55,7 +58,7 @@
</head> </head>
<body> <body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic"> <div class="container template-reference-topic">
<header> <header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="navbar navbar-default navbar-fixed-top" role="navigation">
...@@ -129,8 +132,17 @@ ...@@ -129,8 +132,17 @@
<p>Verifies whether an argument matches formal requirements.</p> <p>Verifies whether an argument matches formal requirements.</p>
</div> </div>
<pre class="usage"><span class='fu'>.check</span>(<span class='no'>x</span>, <span class='no'>type</span>, <span class='kw'>dim</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>miss</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>min</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>max</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <pre class="usage"><span class='fu'>.check</span>(
<span class='kw'>values</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>inf</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>null</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre> <span class='no'>x</span>,
<span class='no'>type</span>,
<span class='kw'>dim</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>miss</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>min</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>max</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>values</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>inf</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>null</span> <span class='kw'>=</span> <span class='fl'>FALSE</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">
...@@ -182,15 +194,12 @@ logical</p></td> ...@@ -182,15 +194,12 @@ logical</p></td>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='kw pkg'>cornet</span><span class='kw ns'>:::</span><span class='fu'><a href='https://rdrr.io/pkg/cornet/man/dot-check.html'>.check</a></span>(<span class='fl'>0.5</span>,<span class='kw'>type</span><span class='kw'>=</span><span class='st'>"scalar"</span>,<span class='kw'>min</span><span class='kw'>=</span><span class='fl'>0</span>,<span class='kw'>max</span><span class='kw'>=</span><span class='fl'>1</span>)</div></pre> <pre class="examples"><div class='input'><span class='kw pkg'>cornet</span><span class='kw ns'>:::</span><span class='fu'>.check</span>(<span class='fl'>0.5</span>,<span class='kw'>type</span><span class='kw'>=</span><span class='st'>"scalar"</span>,<span class='kw'>min</span><span class='kw'>=</span><span class='fl'>0</span>,<span class='kw'>max</span><span class='kw'>=</span><span class='fl'>1</span>)</div></pre>
</div> </div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2> <nav id="toc" data-toggle="toc" class="sticky-top">
<ul class="nav nav-pills nav-stacked"> <h2 data-toc-skip>Contents</h2>
<li><a href="#arguments">Arguments</a></li> </nav>
<li><a href="#examples">Examples</a></li>
</ul>
</div> </div>
</div> </div>
...@@ -201,7 +210,7 @@ logical</p></td> ...@@ -201,7 +210,7 @@ logical</p></td>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div> </div>
</footer> </footer>
......
docs/reference/dot-equal.html
View file @ 7a51fb57
...@@ -10,23 +10,27 @@ ...@@ -10,23 +10,27 @@
<!-- jquery --> <!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap --> <!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" /> <link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
<!-- Font Awesome icons --> <!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
<!-- clipboard.js --> <!-- 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> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
<!-- headroom.js --> <!-- headroom.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown --> <!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet"> <link href="../pkgdown.css" rel="stylesheet">
...@@ -37,7 +41,6 @@ ...@@ -37,7 +41,6 @@
<meta property="og:title" content="Equality — .equal" /> <meta property="og:title" content="Equality — .equal" />
<meta property="og:description" content="Verifies whether two or more arguments are identical." /> <meta property="og:description" content="Verifies whether two or more arguments are identical." />
<meta name="twitter:card" content="summary" />
...@@ -55,7 +58,7 @@ ...@@ -55,7 +58,7 @@
</head> </head>
<body> <body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic"> <div class="container template-reference-topic">
<header> <header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="navbar navbar-default navbar-fixed-top" role="navigation">
...@@ -147,15 +150,12 @@ logical</p></td> ...@@ -147,15 +150,12 @@ logical</p></td>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='kw pkg'>cornet</span><span class='kw ns'>:::</span><span class='fu'><a href='https://rdrr.io/pkg/cornet/man/dot-equal.html'>.equal</a></span>(<span class='fl'>1</span>,<span class='fl'>1</span>,<span class='fl'>1</span>)</div></pre> <pre class="examples"><div class='input'><span class='kw pkg'>cornet</span><span class='kw ns'>:::</span><span class='fu'>.equal</span>(<span class='fl'>1</span>,<span class='fl'>1</span>,<span class='fl'>1</span>)</div></pre>
</div> </div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2> <nav id="toc" data-toggle="toc" class="sticky-top">
<ul class="nav nav-pills nav-stacked"> <h2 data-toc-skip>Contents</h2>
<li><a href="#arguments">Arguments</a></li> </nav>
<li><a href="#examples">Examples</a></li>
</ul>
</div> </div>
</div> </div>
...@@ -166,7 +166,7 @@ logical</p></td> ...@@ -166,7 +166,7 @@ logical</p></td>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div> </div>
</footer> </footer>
......
docs/reference/dot-simulate.html
View file @ 7a51fb57
...@@ -10,23 +10,27 @@ ...@@ -10,23 +10,27 @@
<!-- jquery --> <!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap --> <!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" /> <link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
<!-- Font Awesome icons --> <!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
<!-- clipboard.js --> <!-- 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> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
<!-- headroom.js --> <!-- headroom.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown --> <!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet"> <link href="../pkgdown.css" rel="stylesheet">
...@@ -37,7 +41,6 @@ ...@@ -37,7 +41,6 @@
<meta property="og:title" content="Data simulation — .simulate" /> <meta property="og:title" content="Data simulation — .simulate" />
<meta property="og:description" content="Simulates data for unit tests" /> <meta property="og:description" content="Simulates data for unit tests" />
<meta name="twitter:card" content="summary" />
...@@ -55,7 +58,7 @@ ...@@ -55,7 +58,7 @@
</head> </head>
<body> <body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic"> <div class="container template-reference-topic">
<header> <header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="navbar navbar-default navbar-fixed-top" role="navigation">
...@@ -181,19 +184,14 @@ this function requires the R package MASS ...@@ -181,19 +184,14 @@ this function requires the R package MASS
(see <code><a href='https://rdrr.io/pkg/MASS/man/mvrnorm.html'>mvrnorm</a></code>).</p> (see <code><a href='https://rdrr.io/pkg/MASS/man/mvrnorm.html'>mvrnorm</a></code>).</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='no'>data</span> <span class='kw'>&lt;-</span> <span class='kw pkg'>cornet</span><span class='kw ns'>:::</span><span class='fu'><a href='https://rdrr.io/pkg/cornet/man/dot-simulate.html'>.simulate</a></span>(<span class='kw'>n</span><span class='kw'>=</span><span class='fl'>10</span>,<span class='kw'>p</span><span class='kw'>=</span><span class='fl'>20</span>) <pre class="examples"><div class='input'><span class='no'>data</span> <span class='kw'>&lt;-</span> <span class='kw pkg'>cornet</span><span class='kw ns'>:::</span><span class='fu'>.simulate</span>(<span class='kw'>n</span><span class='kw'>=</span><span class='fl'>10</span>,<span class='kw'>p</span><span class='kw'>=</span><span class='fl'>20</span>)
<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>data</span>)</div><div class='output co'>#&gt; [1] "y" "X" "cutoff"</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>data</span>)</div><div class='output co'>#&gt; [1] "y" "X" "cutoff"</div><div class='input'>
</div></pre> </div></pre>
</div> </div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2> <nav id="toc" data-toggle="toc" class="sticky-top">
<ul class="nav nav-pills nav-stacked"> <h2 data-toc-skip>Contents</h2>
<li><a href="#arguments">Arguments</a></li> </nav>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
</div> </div>
</div> </div>
...@@ -204,7 +202,7 @@ this function requires the R package MASS ...@@ -204,7 +202,7 @@ this function requires the R package MASS
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div> </div>
</footer> </footer>
......
docs/reference/dot-test.html
View file @ 7a51fb57
...@@ -10,23 +10,27 @@ ...@@ -10,23 +10,27 @@
<!-- jquery --> <!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap --> <!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" /> <link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
<!-- Font Awesome icons --> <!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
<!-- clipboard.js --> <!-- 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> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
<!-- headroom.js --> <!-- headroom.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown --> <!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet"> <link href="../pkgdown.css" rel="stylesheet">
...@@ -37,7 +41,6 @@ ...@@ -37,7 +41,6 @@
<meta property="og:title" content="Single-split test — .test" /> <meta property="og:title" content="Single-split test — .test" />
<meta property="og:description" content="Compares models for a continuous response with a cut-off value." /> <meta property="og:description" content="Compares models for a continuous response with a cut-off value." />
<meta name="twitter:card" content="summary" />
...@@ -55,7 +58,7 @@ ...@@ -55,7 +58,7 @@
</head> </head>
<body> <body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic"> <div class="container template-reference-topic">
<header> <header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="navbar navbar-default navbar-fixed-top" role="navigation">
...@@ -178,17 +181,13 @@ use the median \(p\)-value from \(50\) single-split tests ...@@ -178,17 +181,13 @@ use the median \(p\)-value from \(50\) single-split tests
<pre class="examples"><div class='input'><span class='no'>n</span> <span class='kw'>&lt;-</span> <span class='fl'>100</span>; <span class='no'>p</span> <span class='kw'>&lt;-</span> <span class='fl'>200</span> <pre class="examples"><div class='input'><span class='no'>n</span> <span class='kw'>&lt;-</span> <span class='fl'>100</span>; <span class='no'>p</span> <span class='kw'>&lt;-</span> <span class='fl'>200</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='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='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='kw pkg'>cornet</span><span class='kw ns'>:::</span><span class='fu'><a href='https://rdrr.io/pkg/cornet/man/dot-test.html'>.test</a></span>(<span class='kw'>y</span><span class='kw'>=</span><span class='no'>y</span>,<span class='kw'>cutoff</span><span class='kw'>=</span><span class='fl'>0</span>,<span class='kw'>X</span><span class='kw'>=</span><span class='no'>X</span>)</div><div class='img'><img src='dot-test-1.png' alt='' width='700' height='433' /></div><div class='output co'>#&gt; [1] 0.7304053</div><div class='input'> <span class='kw pkg'>cornet</span><span class='kw ns'>:::</span><span class='fu'>.test</span>(<span class='kw'>y</span><span class='kw'>=</span><span class='no'>y</span>,<span class='kw'>cutoff</span><span class='kw'>=</span><span class='fl'>0</span>,<span class='kw'>X</span><span class='kw'>=</span><span class='no'>X</span>)</div><div class='img'><img src='dot-test-1.png' alt='' width='700' height='433' /></div><div class='output co'>#&gt; [1] 0.7304053</div><div class='input'>
</div></pre> </div></pre>
</div> </div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2> <nav id="toc" data-toggle="toc" class="sticky-top">
<ul class="nav nav-pills nav-stacked"> <h2 data-toc-skip>Contents</h2>
<li><a href="#arguments">Arguments</a></li> </nav>
<li><a href="#details">Details</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
</div> </div>
</div> </div>
...@@ -199,7 +198,7 @@ use the median \(p\)-value from \(50\) single-split tests ...@@ -199,7 +198,7 @@ use the median \(p\)-value from \(50\) single-split tests
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div> </div>
</footer> </footer>
......
docs/reference/index.html
View file @ 7a51fb57
...@@ -10,23 +10,27 @@ ...@@ -10,23 +10,27 @@
<!-- jquery --> <!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap --> <!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" /> <link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
<!-- Font Awesome icons --> <!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
<!-- clipboard.js --> <!-- 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> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
<!-- headroom.js --> <!-- headroom.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown --> <!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet"> <link href="../pkgdown.css" rel="stylesheet">
...@@ -53,7 +57,7 @@ ...@@ -53,7 +57,7 @@
</head> </head>
<body> <body data-spy="scroll" data-target="#toc">
<div class="container template-reference-index"> <div class="container template-reference-index">
<header> <header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="navbar navbar-default navbar-fixed-top" role="navigation">
...@@ -136,6 +140,11 @@ ...@@ -136,6 +140,11 @@
<p class="section-desc"></p> <p class="section-desc"></p>
</th> </th>
</tr> </tr>
</tbody><tbody>
<tr> <tr>
<td> <td>
...@@ -174,6 +183,11 @@ ...@@ -174,6 +183,11 @@
<p class="section-desc"></p> <p class="section-desc"></p>
</th> </th>
</tr> </tr>
</tbody><tbody>
<tr> <tr>
<td> <td>
...@@ -209,12 +223,10 @@ ...@@ -209,12 +223,10 @@
</table> </table>
</div> </div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2> <nav id="toc" data-toggle="toc" class="sticky-top">
<ul class="nav nav-pills nav-stacked"> <h2 data-toc-skip>Contents</h2>
<li><a href="#section-user-functions">User functions</a></li> </nav>
<li><a href="#section-internal-functions">Internal functions</a></li>
</ul>
</div> </div>
</div> </div>
...@@ -225,7 +237,7 @@ ...@@ -225,7 +237,7 @@
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div> </div>
</footer> </footer>
......
docs/reference/plot.cornet.html
View file @ 7a51fb57
...@@ -10,23 +10,27 @@ ...@@ -10,23 +10,27 @@
<!-- jquery --> <!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap --> <!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" /> <link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
<!-- Font Awesome icons --> <!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
<!-- clipboard.js --> <!-- 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> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
<!-- headroom.js --> <!-- headroom.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown --> <!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet"> <link href="../pkgdown.css" rel="stylesheet">
...@@ -38,7 +42,6 @@ ...@@ -38,7 +42,6 @@
<meta property="og:title" content="Plot loss matrix — plot.cornet" /> <meta property="og:title" content="Plot loss matrix — plot.cornet" />
<meta property="og:description" content="Plots the loss for different combinations of <meta property="og:description" content="Plots the loss for different combinations of
scaling (sigma) and weighting (pi) parameters." /> scaling (sigma) and weighting (pi) parameters." />
<meta name="twitter:card" content="summary" />
...@@ -56,7 +59,7 @@ scaling (sigma) and weighting (pi) parameters." /> ...@@ -56,7 +59,7 @@ scaling (sigma) and weighting (pi) parameters." />
</head> </head>
<body> <body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic"> <div class="container template-reference-topic">
<header> <header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="navbar navbar-default navbar-fixed-top" role="navigation">
...@@ -132,7 +135,7 @@ scaling (sigma) and weighting (pi) parameters.</p> ...@@ -132,7 +135,7 @@ scaling (sigma) and weighting (pi) parameters.</p>
</div> </div>
<pre class="usage"><span class='co'># S3 method for cornet</span> <pre class="usage"><span class='co'># S3 method for cornet</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>x</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">
...@@ -162,17 +165,13 @@ White always represents high.</p> ...@@ -162,17 +165,13 @@ White always represents high.</p>
<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='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='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'>net</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='cornet.html'>cornet</a></span>(<span class='kw'>y</span><span class='kw'>=</span><span class='no'>y</span>,<span class='kw'>cutoff</span><span class='kw'>=</span><span class='fl'>0</span>,<span class='kw'>X</span><span class='kw'>=</span><span class='no'>X</span>) <span class='no'>net</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='cornet.html'>cornet</a></span>(<span class='kw'>y</span><span class='kw'>=</span><span class='no'>y</span>,<span class='kw'>cutoff</span><span class='kw'>=</span><span class='fl'>0</span>,<span class='kw'>X</span><span class='kw'>=</span><span class='no'>X</span>)
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>net</span>)</div><div class='img'><img src='plot.cornet-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>net</span>)</div><div class='img'><img src='plot.cornet-1.png' alt='' width='700' height='433' /></div><div class='input'>
</div></pre> </div></pre>
</div> </div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2> <nav id="toc" data-toggle="toc" class="sticky-top">
<ul class="nav nav-pills nav-stacked"> <h2 data-toc-skip>Contents</h2>
<li><a href="#arguments">Arguments</a></li> </nav>
<li><a href="#value">Value</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
</div> </div>
</div> </div>
...@@ -183,7 +182,7 @@ White always represents high.</p> ...@@ -183,7 +182,7 @@ White always represents high.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div> </div>
</footer> </footer>
......
docs/reference/predict.cornet.html
View file @ 7a51fb57
...@@ -10,23 +10,27 @@ ...@@ -10,23 +10,27 @@
<!-- jquery --> <!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap --> <!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" /> <link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
<!-- Font Awesome icons --> <!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
<!-- clipboard.js --> <!-- 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> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
<!-- headroom.js --> <!-- headroom.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown --> <!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet"> <link href="../pkgdown.css" rel="stylesheet">
...@@ -37,7 +41,6 @@ ...@@ -37,7 +41,6 @@
<meta property="og:title" content="Predict binary outcome — predict.cornet" /> <meta property="og:title" content="Predict binary outcome — predict.cornet" />
<meta property="og:description" content="Predicts the binary outcome with linear, logistic, and combined regression." /> <meta property="og:description" content="Predicts the binary outcome with linear, logistic, and combined regression." />
<meta name="twitter:card" content="summary" />
...@@ -55,7 +58,7 @@ ...@@ -55,7 +58,7 @@
</head> </head>
<body> <body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic"> <div class="container template-reference-topic">
<header> <header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="navbar navbar-default navbar-fixed-top" role="navigation">
...@@ -270,14 +273,10 @@ and a fixed variance (estimated variance of the numeric outcome).</p> ...@@ -270,14 +273,10 @@ and a fixed variance (estimated variance of the numeric outcome).</p>
#&gt; 100 0.45 0.45 0.4486933</div><div class='input'> #&gt; 100 0.45 0.45 0.4486933</div><div class='input'>
</div></pre> </div></pre>
</div> </div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2> <nav id="toc" data-toggle="toc" class="sticky-top">
<ul class="nav nav-pills nav-stacked"> <h2 data-toc-skip>Contents</h2>
<li><a href="#arguments">Arguments</a></li> </nav>
<li><a href="#details">Details</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
</div> </div>
</div> </div>
...@@ -288,7 +287,7 @@ and a fixed variance (estimated variance of the numeric outcome).</p> ...@@ -288,7 +287,7 @@ and a fixed variance (estimated variance of the numeric outcome).</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div> </div>
</footer> </footer>
......
docs/reference/print.cornet.html
View file @ 7a51fb57
...@@ -10,23 +10,27 @@ ...@@ -10,23 +10,27 @@
<!-- jquery --> <!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap --> <!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" /> <link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
<!-- Font Awesome icons --> <!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
<!-- clipboard.js --> <!-- 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> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
<!-- headroom.js --> <!-- headroom.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown --> <!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet"> <link href="../pkgdown.css" rel="stylesheet">
...@@ -37,7 +41,6 @@ ...@@ -37,7 +41,6 @@
<meta property="og:title" content="Combined regression — print.cornet" /> <meta property="og:title" content="Combined regression — print.cornet" />
<meta property="og:description" content="Prints summary of cornet object." /> <meta property="og:description" content="Prints summary of cornet object." />
<meta name="twitter:card" content="summary" />
...@@ -55,7 +58,7 @@ ...@@ -55,7 +58,7 @@
</head> </head>
<body> <body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic"> <div class="container template-reference-topic">
<header> <header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="navbar navbar-default navbar-fixed-top" role="navigation">
...@@ -167,14 +170,10 @@ and corresponding loss.</p> ...@@ -167,14 +170,10 @@ and corresponding loss.</p>
#&gt; deviance = 1.4</div><div class='input'> #&gt; deviance = 1.4</div><div class='input'>
</div></pre> </div></pre>
</div> </div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2> <nav id="toc" data-toggle="toc" class="sticky-top">
<ul class="nav nav-pills nav-stacked"> <h2 data-toc-skip>Contents</h2>
<li><a href="#arguments">Arguments</a></li> </nav>
<li><a href="#value">Value</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
</div> </div>
</div> </div>
...@@ -185,7 +184,7 @@ and corresponding loss.</p> ...@@ -185,7 +184,7 @@ and corresponding loss.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div> </div>
</footer> </footer>
......
man/cornet.Rd
View file @ 7a51fb57
...@@ -5,9 +5,20 @@ ...@@ -5,9 +5,20 @@
\alias{cornet-package} \alias{cornet-package}
\title{Combined regression} \title{Combined regression}
\usage{ \usage{
cornet(y, cutoff, X, alpha = 1, npi = 101, pi = NULL, nsigma = 99, cornet(
sigma = NULL, nfolds = 10, foldid = NULL, y,
type.measure = "deviance", ...) cutoff,
X,
alpha = 1,
npi = 101,
pi = NULL,
nsigma = 99,
sigma = NULL,
nfolds = 10,
foldid = NULL,
type.measure = "deviance",
...
)
} }
\arguments{ \arguments{
\item{y}{continuous outcome\strong{:} \item{y}{continuous outcome\strong{:}
......
man/cv.cornet.Rd
View file @ 7a51fb57
...@@ -4,9 +4,18 @@ ...@@ -4,9 +4,18 @@
\alias{cv.cornet} \alias{cv.cornet}
\title{Performance measurement} \title{Performance measurement}
\usage{ \usage{
cv.cornet(y, cutoff, X, alpha = 1, nfolds.ext = 5, nfolds.int = 10, cv.cornet(
foldid.ext = NULL, foldid.int = NULL, type.measure = "deviance", y,
...) cutoff,
X,
alpha = 1,
nfolds.ext = 5,
nfolds.int = 10,
foldid.ext = NULL,
foldid.int = NULL,
type.measure = "deviance",
...
)
} }
\arguments{ \arguments{
\item{y}{continuous outcome\strong{:} \item{y}{continuous outcome\strong{:}
......
man/dot-check.Rd
View file @ 7a51fb57
...@@ -4,8 +4,17 @@ ...@@ -4,8 +4,17 @@
\alias{.check} \alias{.check}
\title{Arguments} \title{Arguments}
\usage{ \usage{
.check(x, type, dim = NULL, miss = FALSE, min = NULL, max = NULL, .check(
values = NULL, inf = FALSE, null = FALSE) x,
type,
dim = NULL,
miss = FALSE,
min = NULL,
max = NULL,
values = NULL,
inf = FALSE,
null = FALSE
)
} }
\arguments{ \arguments{
\item{x}{argument} \item{x}{argument}
......
vignettes/application.Rmd
View file @ 7a51fb57
...@@ -9,11 +9,11 @@ vignette: > ...@@ -9,11 +9,11 @@ vignette: >
%\VignetteEngine{knitr::rmarkdown} %\VignetteEngine{knitr::rmarkdown}
--- ---
This script requires that the working directory includes the folders "data", "results", and "manuscript", with the files "PPMI_Baseline_Data_02Jul2018.csv", "PPMI_Year_1-3_Data_02Jul2018.csv" and "PPMI_Data_Dictionary_for_Baseline_Dataset_Jul2018.csv" in the folder "data". We obtained our results using R 3.6.1 (2019-07-05) with cornet 0.0.3 (2019-10-02) on a local machine (x86_64-w64-mingw32/x64, Windows 10 x64). This script requires that the working directory includes the folders "data", "results", and "manuscript", with the files "PPMI_Baseline_Data_02Jul2018.csv", "PPMI_Year_1-3_Data_02Jul2018.csv" and "PPMI_Data_Dictionary_for_Baseline_Dataset_Jul2018.csv" in the folder "data". We obtained our results using R 4.0.0 (2020-04-24) with cornet 0.0.4 (2020-03-08) on a local machine (x86_64-w64-mingw32/x64, Windows 10 x64).
```{r setup, include=FALSE} ```{r setup, include=FALSE}
knitr::opts_chunk$set(echo=TRUE,eval=FALSE) knitr::opts_chunk$set(echo=TRUE,eval=FALSE)
#setwd("C:/Users/armin.rauschenberger/Desktop/cornet") # local drive setwd("C:/Users/armin.rauschenberger/Desktop/cornet") # local drive
#setwd("Z:/Rauschenberger/cornet/BIOINF_20XX-XX-XX") # shared drive #setwd("Z:/Rauschenberger/cornet/BIOINF_20XX-XX-XX") # shared drive
#utils::install.packages(pkgs=c("devtools","missRanger","xtable")) #utils::install.packages(pkgs=c("devtools","missRanger","xtable"))
#devtools::install_github("rauschenberger/cornet") #devtools::install_github("rauschenberger/cornet")
......
vignettes/simulation.Rmd
View file @ 7a51fb57
...@@ -9,11 +9,11 @@ vignette: > ...@@ -9,11 +9,11 @@ vignette: >
%\VignetteEngine{knitr::rmarkdown} %\VignetteEngine{knitr::rmarkdown}
--- ---
This script requires that the working directory includes the folders "data", "results", and "manuscript". We obtained our results using R 3.6.1 (2019-07-05) with cornet 0.0.3 (2019-10-02) on a local machine (x86_64-w64-mingw32/x64, Windows 10 x64), and verified them on a virtual machine (x86_64-pc-linux-gnu, Ubuntu 16.04.6). Floating point errors might lead to slightly different results on other platforms. This script requires that the working directory includes the folders "data", "results", and "manuscript". We obtained our results using R 4.0.0 (2020-04-24) with cornet 0.0.4 (2020-03-18) on a local machine (x86_64-w64-mingw32/x64, Windows 10 x64). Floating point errors might lead to slightly different results on other platforms.
```{r setup,include=FALSE} ```{r setup,include=FALSE}
knitr::opts_chunk$set(echo=TRUE,eval=FALSE) knitr::opts_chunk$set(echo=TRUE,eval=FALSE)
#setwd("C:/Users/armin.rauschenberger/Desktop/cornet") # local drive setwd("C:/Users/armin.rauschenberger/Desktop/cornet") # local drive
#setwd("Z:/Rauschenberger/cornet/BIOINF_20XX-XX-XX") # shared drive #setwd("Z:/Rauschenberger/cornet/BIOINF_20XX-XX-XX") # shared drive
#devtools::install_github("rauschenberger/cornet") #devtools::install_github("rauschenberger/cornet")
``` ```
...@@ -71,19 +71,25 @@ graphics::axis(side=2) ...@@ -71,19 +71,25 @@ graphics::axis(side=2)
graphics::abline(h=0,col="grey",lty=2) graphics::abline(h=0,col="grey",lty=2)
graphics::abline(v=at+1,col="grey",lty=2) graphics::abline(v=at+1,col="grey",lty=2)
graphics::box() graphics::box()
graphics::boxplot(fuse1,at=at-0.5,add=TRUE,axes=FALSE,border="black") graphics::boxplot(fuse1,at=at-0.5,add=TRUE,axes=FALSE,col="white",border="black")
graphics::boxplot(fuse0,at=at+0.5,add=TRUE,axes=FALSE,border="darkgrey") graphics::boxplot(fuse0,at=at+0.5,add=TRUE,axes=FALSE,col="white",border="darkgrey")
labels <- names(fuse1) labels <- names(fuse1)
labels <- ifelse(labels=="class","mcr",labels) labels <- ifelse(labels=="class","mcr",labels)
labels <- ifelse(labels %in% c("mcr","mse","mae","auc"),toupper(labels),labels) labels <- ifelse(labels %in% c("mcr","mse","mae","auc"),toupper(labels),labels)
graphics::axis(side=1,at=at,labels=labels) graphics::axis(side=1,at=at,labels=labels)
grDevices::dev.off() grDevices::dev.off()
# decrease
sapply(fuse1,function(x) mean(x<0)) # lasso sapply(fuse1,function(x) mean(x<0)) # lasso
sapply(fuse0,function(x) mean(x<0)) # ridge sapply(fuse0,function(x) mean(x<0)) # ridge
# constant
sapply(fuse1,function(x) mean(x==0)) # lasso sapply(fuse1,function(x) mean(x==0)) # lasso
sapply(fuse0,function(x) mean(x==0)) # ridge sapply(fuse0,function(x) mean(x==0)) # ridge
# increase
sapply(fuse1,function(x) mean(x>0)) # lasso
sapply(fuse0,function(x) mean(x>0)) # ridge
``` ```
```{r figure_TAB} ```{r figure_TAB}
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment