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Commit 009ca032 authored by Armin Rauschenberger's avatar Armin Rauschenberger
Browse files

automation

parent ce0ec81c
......@@ -10,6 +10,6 @@ Authors@R: person("Armin","Rauschenberger",email="a.rauschenberger@vumc.nl",role
VignetteBuilder: knitr
License: GPL-3
LazyData: true
RoxygenNote: 6.1.0
RoxygenNote: 6.1.1
URL: https://github.com/rauschenberger/cornet
BugReports: https://github.com/rauschenberger/cornet/issues
......@@ -7,19 +7,19 @@
#' Combined regression
#'
#' @description
#' Implements logistic regression for dichotomised outcomes
#' Implements logistic regression for dichotomised outcomes
#' in high-dimensional settings.
#'
#' @param y
#' continuous response\strong{:}
#' continuous outcome\strong{:}
#' vector of length \eqn{n}
#'
#' @param cutoff
#' cutoff point for dichotomising response into classes\strong{:}
#' cutoff point for dichotomising outcome into classes\strong{:}
#' \emph{meaningful} value between \code{min(y)} and \code{max(y)}
#'
#' @param X
#' covariates\strong{:}
#' features\strong{:}
#' numeric matrix with \eqn{n} rows (samples)
#' and \eqn{p} columns (variables)
#'
......@@ -63,7 +63,7 @@
#' and a \emph{binomial} model for the binary response,
#' meaning that the \code{glmnet} argument \code{family} is unavailable.
#' Even if \code{type.measure} equals \code{"deviance"},
#' the loss is uncomparable between linear and logistic regression.
#' the loss is incomparable between linear and logistic regression.
#'
#' @return
#' Returns an object of class \code{cornet}, a list with multiple slots:
......@@ -524,6 +524,8 @@ predict.cornet <- function(object,newx,type="probability",...){
#' @examples
#' cornet:::.check(0.5,type="scalar",min=0,max=1)
#'
#' #.check(x=c(1,2,3,4,45),type="vector",values=1:10)
#'
.check <- function(x,type,miss=FALSE,min=NULL,max=NULL,values=NULL,inf=FALSE,null=FALSE){
name <- deparse(substitute(x))
if(null && is.null(x)){
......@@ -552,7 +554,7 @@ predict.cornet <- function(object,newx,type="probability",...){
if(!is.null(max) && any(x>max)){
stop(paste0("expecting ",name," <= ",max),call.=FALSE)
}
if(!is.null(values) && !(x %in% values)){
if(!is.null(values) && any(!x %in% values)){
stop(paste0("Argument \"",name,"\" contains invalid values."),call.=FALSE)
}
if(!inf && any(is.infinite(values))){
......@@ -561,7 +563,6 @@ predict.cornet <- function(object,newx,type="probability",...){
return(invisible(NULL))
}
#--- Application ---------------------------------------------------------------
#' @title
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......@@ -129,9 +131,8 @@
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......@@ -93,10 +94,10 @@
<h2 class="hasAnchor">
<a href="#installation" class="anchor"></a>Installation</h2>
<p>Installing the current release from <a href="https://CRAN.R-project.org/package=cornet">CRAN</a>:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">install.packages</span>(<span class="st">"cornet"</span>)</code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"cornet"</span>)</code></pre></div>
<p>Installing the latest development version from <a href="https://github.com/rauschenberger/cornet">GitHub</a>:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co">#install.packages("devtools")</span>
<span class="kw">library</span>(devtools)
<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(devtools)
<span class="kw">install_github</span>(<span class="st">"rauschenberger/cornet"</span>)</code></pre></div>
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......@@ -119,9 +120,8 @@
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<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. (Such outcomes are not naturally but artificially binary.)">
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......@@ -22,14 +22,15 @@
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</span>
</div>
......@@ -93,10 +94,10 @@
<h2 class="hasAnchor">
<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>, or the latest development version from <a href="https://github.com/rauschenberger/cornet">GitHub</a>:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">install.packages</span>(<span class="st">"cornet"</span>)
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"cornet"</span>)
<span class="co">#install.packages("devtools")</span>
devtools<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/reexports">install_github</a></span>(<span class="st">"rauschenberger/cornet"</span>)</code></pre></div>
devtools<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/devtools/topics/reexports">install_github</a></span>(<span class="st">"rauschenberger/cornet"</span>)</code></pre></div>
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......@@ -146,9 +147,8 @@ devtools<span class="op">::</span><span class="kw"><a href="http://www.rdocument
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<title>Changelog • cornet</title>
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......@@ -35,7 +35,8 @@
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......@@ -139,9 +141,8 @@
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......@@ -58,9 +58,14 @@ img {
max-width: 100%;
}
/* Fix bug in bootstrap (only seen in firefox) */
summary {
display: list-item;
}
/* Typographic tweaking ---------------------------------*/
.contents h1.page-header {
.contents .page-header {
margin-top: calc(-60px + 1em);
}
......@@ -136,10 +141,9 @@ a.anchor {
.ref-index th {font-weight: normal;}
.ref-index td {vertical-align: top;}
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......
......@@ -25,9 +25,13 @@
for (var i = 0; i < links.length; i++) {
if (links[i].getAttribute("href") === "#")
continue;
var path = paths(links[i].pathname);
// Ignore external links
if (links[i].host !== location.host)
continue;
var nav_path = paths(links[i].pathname);
var length = prefix_length(cur_path, path);
var length = prefix_length(nav_path, cur_path);
if (length > max_length) {
max_length = length;
pos = i;
......@@ -52,13 +56,14 @@
return(pieces);
}
// Returns -1 if not found
function prefix_length(needle, haystack) {
if (needle.length > haystack.length)
return(0);
return(-1);
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return(needle.length === 0 ? 1 : 0);
return(needle.length === 0 ? 0 : -1);
}
for (var i = 0; i < haystack.length; i++) {
......@@ -78,9 +83,9 @@
element.setAttribute('data-original-title', tooltipOriginalTitle);
}
if(Clipboard.isSupported()) {
if(ClipboardJS.isSupported()) {
$(document).ready(function() {
var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
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$(".examples, div.sourceCode").addClass("hasCopyButton");
......@@ -91,7 +96,7 @@
$('.btn-copy-ex').tooltip({container: 'body'});
// Initialize clipboard:
var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
var clipboardBtnCopies = new ClipboardJS('[data-clipboard-copy]', {
text: function(trigger) {
return trigger.parentNode.textContent;
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......
pandoc: 1.19.2.1
pkgdown: 1.1.0
pkgdown: 1.3.0
pkgdown_sha: ~
articles:
vignette: vignette.html
articles: []
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......@@ -9,17 +9,17 @@
<title>Extract estimated coefficients — coef.cornet • cornet</title>
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......@@ -39,7 +39,8 @@ under the penalty parameter that minimises the cross-validated loss." />
<!-- mathjax -->
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......@@ -55,14 +56,15 @@ under the penalty parameter that minimises the cross-validated loss." />
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<div class="container">
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<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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<span class="sr-only">Toggle navigation</span>
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<span class="icon-bar"></span>
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">cornet</a>
<span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.0.1</span>
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</span>
</div>
......@@ -126,14 +128,14 @@ under the penalty parameter that minimises the cross-validated loss.</p>
</div>
<pre class="usage"><span class='co'># S3 method for cornet</span>
<span class='fu'>coef</span>(<span class='no'>object</span>, <span class='no'>...</span>)</pre>
<span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>object</span>, <span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>object</th>
<td><p><a href='cornet.html'>cornet</a> object</p></td>
<td><p>cornet object</p></td>
</tr>
<tr>
<th>...</th>
......@@ -172,9 +174,8 @@ and logistic (second column, <code>"gamma"</code>) regression.</p>
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<p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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......@@ -9,17 +9,17 @@
<title>Combined regression — cornet • cornet</title>
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