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Commit bcfdcc05 authored by Armin Rauschenberger's avatar Armin Rauschenberger
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R/functions.R
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......@@ -277,11 +277,11 @@ cornet <- function(y,cutoff,X,alpha=1,npi=101,pi=NULL,nsigma=99,sigma=NULL,nfold
#' and corresponding loss.
#'
#' @examples
#' \donttest{n <- 100; p <- 200
#' n <- 100; p <- 200
#' y <- rnorm(n)
#' X <- matrix(rnorm(n*p),nrow=n,ncol=p)
#' net <- cornet(y=y,cutoff=0,X=X)
#' print(net)}
#' print(net)
#'
print.cornet <- function(x,...){
cat("cornet object:\n")
......@@ -313,15 +313,15 @@ print.cornet <- function(x,...){
#' @return
#' This function returns a matrix with \eqn{n} rows and two columns,
#' where \eqn{n} is the sample size. It includes the estimated coefficients
#' from linear regression (1st column, \code{"beta"})
#' and logistic regression (2nd column, \code{"gamma"}).
#' from linear regression (1st column: \code{"beta"})
#' and logistic regression (2nd column: \code{"gamma"}).
#'
#' @examples
#' \donttest{n <- 100; p <- 200
#' n <- 100; p <- 200
#' y <- rnorm(n)
#' X <- matrix(rnorm(n*p),nrow=n,ncol=p)
#' net <- cornet(y=y,cutoff=0,X=X)
#' coef(net)}
#' coef(net)
#'
coef.cornet <- function(object,...){
......@@ -362,11 +362,11 @@ coef.cornet <- function(object,...){
#' White always represents high.
#'
#' @examples
#' \donttest{n <- 100; p <- 200
#' n <- 100; p <- 200
#' y <- rnorm(n)
#' X <- matrix(rnorm(n*p),nrow=n,ncol=p)
#' net <- cornet(y=y,cutoff=0,X=X)
#' plot(net)}
#' plot(net)
#'
plot.cornet <- function(x,...){
......@@ -446,11 +446,11 @@ plot.cornet <- function(x,...){
#' further arguments (not applicable)
#'
#' @examples
#' \donttest{n <- 100; p <- 200
#' n <- 100; p <- 200
#' y <- rnorm(n)
#' X <- matrix(rnorm(n*p),nrow=n,ncol=p)
#' net <- cornet(y=y,cutoff=0,X=X)
#' predict(net,newx=X)}
#' predict(net,newx=X)
#'
predict.cornet <- function(object,newx,type="probability",...){
......@@ -651,6 +651,11 @@ predict.cornet <- function(object,newx,type="probability",...){
#' @inheritParams cornet
#'
#' @examples
#' \dontshow{n <- 100; p <- 20
#' y <- rnorm(n)
#' X <- matrix(rnorm(n*p),nrow=n,ncol=p)
#' loss <- cornet:::.compare(y=y,cutoff=0,X=X,nfolds=2)
#' loss}
#' \donttest{n <- 100; p <- 200
#' y <- rnorm(n)
#' X <- matrix(rnorm(n*p),nrow=n,ncol=p)
......@@ -727,10 +732,10 @@ predict.cornet <- function(object,newx,type="probability",...){
#' @inheritParams cornet
#'
#' @examples
#' \donttest{n <- 100; p <- 200
#' n <- 100; p <- 200
#' y <- rnorm(n)
#' X <- matrix(rnorm(n*p),nrow=n,ncol=p)
#' cornet:::.test(y=y,cutoff=0,X=X)}
#' cornet:::.test(y=y,cutoff=0,X=X)
#'
.test <- function(y,cutoff,X,alpha=1,type.measure="deviance"){
......@@ -795,6 +800,7 @@ predict.cornet <- function(object,newx,type="probability",...){
return(invisible(list(y=y,X=X)))
}
#--- Legacy --------------------------------------------------------------------
# # Import this function from the palasso package.
......
cran-comments.md
View file @ bcfdcc05
Thanks for your suggestions!
Thanks!
# Changes
- More details in description field.
- Reference in description field.
- Executable examples in all help files.
- examples without \donttest{}, or with \donttest{} and \dontshow{}
# Notes
......
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......@@ -22,15 +22,14 @@
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......@@ -110,8 +109,9 @@
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......@@ -126,8 +124,9 @@
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......@@ -88,10 +87,10 @@
<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>:</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://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"cornet"</span>)</a></code></pre></div>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw">install.packages</span>(<span class="st">"cornet"</span>)</a></code></pre></div>
<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>
<a class="sourceLine" id="cb2-2" title="2">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>)</a></code></pre></div>
<a class="sourceLine" id="cb2-2" title="2">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>)</a></code></pre></div>
<p>Armin Rauschenberger and Enrico Glaab (2019). “Lasso and ridge regression for dichotomised outcomes”. <em>Manuscript in preparation.</em></p>
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......@@ -35,8 +35,7 @@
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......@@ -126,8 +124,9 @@
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<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.">
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......@@ -88,10 +87,10 @@
<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>:</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://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"cornet"</span>)</a></code></pre></div>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw">install.packages</span>(<span class="st">"cornet"</span>)</a></code></pre></div>
<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>
<a class="sourceLine" id="cb2-2" title="2">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>)</a></code></pre></div>
<a class="sourceLine" id="cb2-2" title="2">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>)</a></code></pre></div>
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......@@ -144,8 +143,9 @@
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......@@ -135,8 +133,9 @@
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......@@ -56,14 +52,13 @@
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......@@ -83,9 +78,9 @@
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<title>Extract estimated coefficients — coef.cornet • cornet</title>
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