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Commit bcfdcc05 authored by Armin Rauschenberger's avatar Armin Rauschenberger
Browse files

automation

parent 958b5725
...@@ -277,11 +277,11 @@ cornet <- function(y,cutoff,X,alpha=1,npi=101,pi=NULL,nsigma=99,sigma=NULL,nfold ...@@ -277,11 +277,11 @@ cornet <- function(y,cutoff,X,alpha=1,npi=101,pi=NULL,nsigma=99,sigma=NULL,nfold
#' and corresponding loss. #' and corresponding loss.
#' #'
#' @examples #' @examples
#' \donttest{n <- 100; p <- 200 #' n <- 100; p <- 200
#' y <- rnorm(n) #' y <- rnorm(n)
#' X <- matrix(rnorm(n*p),nrow=n,ncol=p) #' X <- matrix(rnorm(n*p),nrow=n,ncol=p)
#' net <- cornet(y=y,cutoff=0,X=X) #' net <- cornet(y=y,cutoff=0,X=X)
#' print(net)} #' print(net)
#' #'
print.cornet <- function(x,...){ print.cornet <- function(x,...){
cat("cornet object:\n") cat("cornet object:\n")
...@@ -313,15 +313,15 @@ print.cornet <- function(x,...){ ...@@ -313,15 +313,15 @@ print.cornet <- function(x,...){
#' @return #' @return
#' This function returns a matrix with \eqn{n} rows and two columns, #' This function returns a matrix with \eqn{n} rows and two columns,
#' where \eqn{n} is the sample size. It includes the estimated coefficients #' where \eqn{n} is the sample size. It includes the estimated coefficients
#' from linear regression (1st column, \code{"beta"}) #' from linear regression (1st column: \code{"beta"})
#' and logistic regression (2nd column, \code{"gamma"}). #' and logistic regression (2nd column: \code{"gamma"}).
#' #'
#' @examples #' @examples
#' \donttest{n <- 100; p <- 200 #' n <- 100; p <- 200
#' y <- rnorm(n) #' y <- rnorm(n)
#' X <- matrix(rnorm(n*p),nrow=n,ncol=p) #' X <- matrix(rnorm(n*p),nrow=n,ncol=p)
#' net <- cornet(y=y,cutoff=0,X=X) #' net <- cornet(y=y,cutoff=0,X=X)
#' coef(net)} #' coef(net)
#' #'
coef.cornet <- function(object,...){ coef.cornet <- function(object,...){
...@@ -362,11 +362,11 @@ coef.cornet <- function(object,...){ ...@@ -362,11 +362,11 @@ coef.cornet <- function(object,...){
#' White always represents high. #' White always represents high.
#' #'
#' @examples #' @examples
#' \donttest{n <- 100; p <- 200 #' n <- 100; p <- 200
#' y <- rnorm(n) #' y <- rnorm(n)
#' X <- matrix(rnorm(n*p),nrow=n,ncol=p) #' X <- matrix(rnorm(n*p),nrow=n,ncol=p)
#' net <- cornet(y=y,cutoff=0,X=X) #' net <- cornet(y=y,cutoff=0,X=X)
#' plot(net)} #' plot(net)
#' #'
plot.cornet <- function(x,...){ plot.cornet <- function(x,...){
...@@ -446,11 +446,11 @@ plot.cornet <- function(x,...){ ...@@ -446,11 +446,11 @@ plot.cornet <- function(x,...){
#' further arguments (not applicable) #' further arguments (not applicable)
#' #'
#' @examples #' @examples
#' \donttest{n <- 100; p <- 200 #' n <- 100; p <- 200
#' y <- rnorm(n) #' y <- rnorm(n)
#' X <- matrix(rnorm(n*p),nrow=n,ncol=p) #' X <- matrix(rnorm(n*p),nrow=n,ncol=p)
#' net <- cornet(y=y,cutoff=0,X=X) #' net <- cornet(y=y,cutoff=0,X=X)
#' predict(net,newx=X)} #' predict(net,newx=X)
#' #'
predict.cornet <- function(object,newx,type="probability",...){ predict.cornet <- function(object,newx,type="probability",...){
...@@ -651,6 +651,11 @@ predict.cornet <- function(object,newx,type="probability",...){ ...@@ -651,6 +651,11 @@ predict.cornet <- function(object,newx,type="probability",...){
#' @inheritParams cornet #' @inheritParams cornet
#' #'
#' @examples #' @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 #' \donttest{n <- 100; p <- 200
#' y <- rnorm(n) #' y <- rnorm(n)
#' X <- matrix(rnorm(n*p),nrow=n,ncol=p) #' X <- matrix(rnorm(n*p),nrow=n,ncol=p)
...@@ -727,10 +732,10 @@ predict.cornet <- function(object,newx,type="probability",...){ ...@@ -727,10 +732,10 @@ predict.cornet <- function(object,newx,type="probability",...){
#' @inheritParams cornet #' @inheritParams cornet
#' #'
#' @examples #' @examples
#' \donttest{n <- 100; p <- 200 #' n <- 100; p <- 200
#' y <- rnorm(n) #' y <- rnorm(n)
#' X <- matrix(rnorm(n*p),nrow=n,ncol=p) #' 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"){ .test <- function(y,cutoff,X,alpha=1,type.measure="deviance"){
...@@ -795,6 +800,7 @@ predict.cornet <- function(object,newx,type="probability",...){ ...@@ -795,6 +800,7 @@ predict.cornet <- function(object,newx,type="probability",...){
return(invisible(list(y=y,X=X))) return(invisible(list(y=y,X=X)))
} }
#--- Legacy -------------------------------------------------------------------- #--- Legacy --------------------------------------------------------------------
# # Import this function from the palasso package. # # Import this function from the palasso package.
......
Thanks for your suggestions! Thanks!
# Changes # Changes
- More details in description field. - examples without \donttest{}, or with \donttest{} and \dontshow{}
- Reference in description field.
- Executable examples in all help files.
# Notes # Notes
......
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...@@ -22,15 +22,14 @@ ...@@ -22,15 +22,14 @@
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...@@ -110,8 +109,9 @@ ...@@ -110,8 +109,9 @@
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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......
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...@@ -9,17 +9,17 @@ ...@@ -9,17 +9,17 @@
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...@@ -35,8 +35,7 @@ ...@@ -35,8 +35,7 @@
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...@@ -88,10 +87,10 @@ ...@@ -88,10 +87,10 @@
<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://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> <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="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> <p>Armin Rauschenberger and Enrico Glaab (2019). “Lasso and ridge regression for dichotomised outcomes”. <em>Manuscript in preparation.</em></p>
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...@@ -114,8 +113,9 @@ ...@@ -114,8 +113,9 @@
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...@@ -88,10 +87,10 @@ ...@@ -88,10 +87,10 @@
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<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://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span