automation

DESCRIPTION

@@ -6,7 +6,7 @@ Depends: R (>= 3.0.0)
 Imports: glmnet, palasso, cornet
 Suggests: knitr, testthat, MASS
 Enhances: spls, SiER, MRCE
-Authors@R: person("Armin","Rauschenberger",email="a.rauschenberger@vumc.nl",role=c("aut","cre"))
+Authors@R: person("Armin","Rauschenberger",email="armin.rauschenberger@uni.lu",role=c("aut","cre"))
 VignetteBuilder: knitr
 License: GPL-3
 LazyData: true

R/functions.R

 
-#.loss <- get(".loss",envir=asNamespace("palasso"))
-#.folds <- get(".folds",envir=asNamespace("palasso"))
-#.check <- get(".check",envir=asNamespace("cornet"))
+# import unexported functions:
+# FUNCTION <- get("FUNCTION",envir=asNamespace("PACKAGE"))
 
 #--- Main function -------------------------------------------------------------
 
 #' @export
-#' @aliases joinet-package
 #' @title
 #' Multivariate Elastic Net Regression
 #' 

R/pkgname.R

+
+#' @name joinet-package
+#' @keywords documentation
+#' @docType package
+#' 
+#' @title
+#' Multivariate Elastic Net Regression
+#' 
+#' @description
+#' The R package \code{joinet} implements multivariate
+#' ridge and lasso regression using stacked generalisation.
+#' This multivariate regression typically outperforms
+#' univariate regression at predicting correlated outcomes.
+#' It provides predictive and interpretable models
+#' in high-dimensional settings.
+#' 
+#' @details
+#' Use function \code{\link{joinet}} for model fitting.
+#' Type \code{library(joinet)} and then \code{?joinet} or
+#' \code{help("joinet)"} to open its help file.
+#' 
+#' See the vignette for further examples.
+#' Type \code{vignette("joinet")} or \code{browseVignettes("joinet")}
+#' to open the vignette.
+#' 
+#' @references
+#' Armin Rauschenberger and Enrico Glaab (2019).
+#' "joinet: predicting correlated outcomes jointly to improve clinical prognosis".
+#' \emph{Manuscript in preparation}.
+#' 
+#' \email{armin.rauschenberger@uni.lu}
+#'
+#' @examples
+#' #--- data simulation ---
+#' n <- 50; p <- 100; q <- 3
+#' X <- matrix(rnorm(n*p),nrow=n,ncol=p)
+#' Y <- replicate(n=q,expr=rnorm(n=n,mean=rowSums(X[,1:5])))
+#' # n samples, p inputs, q outputs
+#' 
+#' #--- model fitting ---
+#' object <- joinet(Y=Y,X=X)
+#' # slot "base": univariate
+#' # slot "meta": multivariate
+#' 
+#' #--- make predictions ---
+#' y_hat <- predict(object,newx=X)
+#' # n x q matrix "base": univariate
+#' # n x q matrix "meta": multivariate 
+#' 
+#' #--- extract coefficients ---
+#' coef <- coef(object)
+#' # effects of inputs on outputs
+#' # q vector "alpha": intercepts
+#' # p x q matrix "beta": slopes
+#' 
+#' #--- model comparison ---
+#' loss <- cv.joinet(Y=Y,X=X)
+#' # cross-validated loss
+#' # row "base": univariate
+#' # row "meta": multivariate
+#' 
+NULL
+

_pkgdown.yml

@@ -17,7 +17,7 @@ navbar:
     - text: "functions"
       href: reference/index.html
     - text: "vignette"
-      href: articles/vignette.html
+      href: articles/joinet.html
     - text: "article"
       href: articles/article.html
     - text: "news"
@@ -29,12 +29,11 @@ navbar:
       href: https://cran.r-project.org/package=joinet
 
 reference:
-  - title: "User functions"
+  - title: "Functions"
     contents:
       - joinet
       - predict.joinet
       - coef.joinet
       - weights.joinet
-  - title: "Internal functions"
-    contents:
       - cv.joinet
+      - joinet-package

cran-comments.md

 
 # Notes
 
-- Early update because of manuscript submission (examples, vignettes).
-
-- The maintainer email will change to armin.rauschenberger@uni.lu.
\ No newline at end of file
+Please accept ::: calls to "palasso" and "cornet",
+as maintainer email changes for all packages.
\ No newline at end of file

docs/articles/article.html

@@ -40,7 +40,7 @@
   <a href="../reference/index.html">functions</a>
 </li>
 <li>
-  <a href="../articles/vignette.html">vignette</a>
+  <a href="../articles/joinet.html">vignette</a>
 </li>
 <li>
   <a href="../articles/article.html">article</a>

docs/articles/index.html

@@ -70,7 +70,7 @@
   <a href="../reference/index.html">functions</a>
 </li>
 <li>
-  <a href="../articles/vignette.html">vignette</a>
+  <a href="../articles/joinet.html">vignette</a>
 </li>
 <li>
   <a href="../articles/article.html">article</a>
@@ -114,7 +114,7 @@
 
       <ul>
         <li><a href="article.html">Multivariate Elastic Net Regression</a></li>
-        <li><a href="vignette.html">Multivariate Elastic Net Regression</a></li>
+        <li><a href="joinet.html">Multivariate Elastic Net Regression</a></li>
       </ul>
     </div>
   </div>

docs/articles/vignette.html → docs/articles/joinet.html

@@ -40,7 +40,7 @@
   <a href="../reference/index.html">functions</a>
 </li>
 <li>
-  <a href="../articles/vignette.html">vignette</a>
+  <a href="../articles/joinet.html">vignette</a>
 </li>
 <li>
   <a href="../articles/article.html">article</a>
@@ -77,8 +77,8 @@
       <h1>Multivariate Elastic Net Regression</h1>
             
       
-      <small class="dont-index">Source: <a href="https://github.com/rauschenberger/joinet/blob/master/vignettes/vignette.Rmd"><code>vignettes/vignette.Rmd</code></a></small>
-      <div class="hidden name"><code>vignette.Rmd</code></div>
+      <small class="dont-index">Source: <a href="https://github.com/rauschenberger/joinet/blob/master/vignettes/joinet.Rmd"><code>vignettes/joinet.Rmd</code></a></small>
+      <div class="hidden name"><code>joinet.Rmd</code></div>
 
     </div>
 

docs/authors.html

@@ -70,7 +70,7 @@
   <a href="reference/index.html">functions</a>
 </li>
 <li>
-  <a href="articles/vignette.html">vignette</a>
+  <a href="articles/joinet.html">vignette</a>
 </li>
 <li>
   <a href="articles/article.html">article</a>

docs/index.html

@@ -40,7 +40,7 @@
   <a href="reference/index.html">functions</a>
 </li>
 <li>
-  <a href="articles/vignette.html">vignette</a>
+  <a href="articles/joinet.html">vignette</a>
 </li>
 <li>
   <a href="articles/article.html">article</a>

docs/news/index.html

@@ -70,7 +70,7 @@
   <a href="../reference/index.html">functions</a>
 </li>
 <li>
-  <a href="../articles/vignette.html">vignette</a>
+  <a href="../articles/joinet.html">vignette</a>
 </li>
 <li>
   <a href="../articles/article.html">article</a>

docs/pkgdown.yml

@@ -3,5 +3,5 @@ pkgdown: 1.3.0
 pkgdown_sha: ~
 articles:
   article: article.html
-  vignette: vignette.html
+  joinet: joinet.html
 

docs/reference/coef.joinet.html

@@ -75,7 +75,7 @@ the coefficients from the base learners.)" />
   <a href="../reference/index.html">functions</a>
 </li>
 <li>
-  <a href="../articles/vignette.html">vignette</a>
+  <a href="../articles/joinet.html">vignette</a>
 </li>
 <li>
   <a href="../articles/article.html">article</a>

docs/reference/cv.joinet.html

@@ -73,7 +73,7 @@
   <a href="../reference/index.html">functions</a>
 </li>
 <li>
-  <a href="../articles/vignette.html">vignette</a>
+  <a href="../articles/joinet.html">vignette</a>
 </li>
 <li>
   <a href="../articles/article.html">article</a>

docs/reference/index.html

@@ -70,7 +70,7 @@
   <a href="../reference/index.html">functions</a>
 </li>
 <li>
-  <a href="../articles/vignette.html">vignette</a>
+  <a href="../articles/joinet.html">vignette</a>
 </li>
 <li>
   <a href="../articles/article.html">article</a>
@@ -119,7 +119,7 @@
     <tbody>
       <tr>
         <th colspan="2">
-          <h2 id="section-user-functions" class="hasAnchor"><a href="#section-user-functions" class="anchor"></a>User functions</h2>
+          <h2 id="section-functions" class="hasAnchor"><a href="#section-functions" class="anchor"></a>Functions</h2>
           <p class="section-desc"></p>
         </th>
       </tr>
@@ -147,20 +147,18 @@
           <p><code><a href="weights.joinet.html">weights(<i>&lt;joinet&gt;</i>)</a></code> </p>
         </td>
         <td><p>Extract Weights</p></td>
-      </tr>
-    </tbody><tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-internal-functions" class="hasAnchor"><a href="#section-internal-functions" class="anchor"></a>Internal functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
+      </tr><tr>
         
         <td>
           <p><code><a href="cv.joinet.html">cv.joinet()</a></code> </p>
         </td>
         <td><p>Model comparison</p></td>
+      </tr><tr>
+        
+        <td>
+          <p><code><a href="joinet-package.html">joinet-package</a></code> </p>
+        </td>
+        <td><p>Multivariate Elastic Net Regression</p></td>
       </tr>
     </tbody>
     </table>
@@ -169,8 +167,7 @@
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
     <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-user-functions">User functions</a></li>
-      <li><a href="#section-internal-functions">Internal functions</a></li>
+      <li><a href="#section-functions">Functions</a></li>
     </ul>
   </div>
 </div>

docs/reference/joinet.html

@@ -73,7 +73,7 @@
   <a href="../reference/index.html">functions</a>
 </li>
 <li>
-  <a href="../articles/vignette.html">vignette</a>
+  <a href="../articles/joinet.html">vignette</a>
 </li>
 <li>
   <a href="../articles/article.html">article</a>

docs/reference/weights.joinet.html

@@ -74,7 +74,7 @@ i.e. the weights for the base learners." />
   <a href="../reference/index.html">functions</a>
 </li>
 <li>
-  <a href="../articles/vignette.html">vignette</a>
+  <a href="../articles/joinet.html">vignette</a>
 </li>
 <li>
   <a href="../articles/article.html">article</a>
@@ -152,11 +152,11 @@ in the row on the outcomes in the column.</p>
 <span class='no'>X</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/matrix'>matrix</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/Normal'>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'>Y</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/lapply'>replicate</a></span>(<span class='kw'>n</span><span class='kw'>=</span><span class='no'>q</span>,<span class='kw'>expr</span><span class='kw'>=</span><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/Normal'>rnorm</a></span>(<span class='kw'>n</span><span class='kw'>=</span><span class='no'>n</span>,<span class='kw'>mean</span><span class='kw'>=</span><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/colSums'>rowSums</a></span>(<span class='no'>X</span>[,<span class='fl'>1</span>:<span class='fl'>5</span>])))
 <span class='no'>object</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='joinet.html'>joinet</a></span>(<span class='kw'>Y</span><span class='kw'>=</span><span class='no'>Y</span>,<span class='kw'>X</span><span class='kw'>=</span><span class='no'>X</span>)
-<span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/weights'>weights</a></span>(<span class='no'>object</span>)</div><div class='output co'>#&gt;                    y1        y2        y3
-#&gt; (Intercept) 0.4123532 0.2048455 0.3295532
-#&gt; V1          0.3347547 0.7144811 0.4977934
-#&gt; V2          0.4795655 0.1919470 0.3724097
-#&gt; V3          0.6110722 0.4751144 0.4351376</div><div class='input'>
+<span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/weights'>weights</a></span>(<span class='no'>object</span>)</div><div class='output co'>#&gt;                    y1         y2        y3
+#&gt; (Intercept) 0.1407709 -0.2016272 0.3005088
+#&gt; V1          0.5225819  0.5461316 0.3397260
+#&gt; V2          0.3307281  0.2754751 0.4911718
+#&gt; V3          0.3925573  0.2745159 0.3276262</div><div class='input'>
 </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">

man/joinet-package.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/pkgname.R
+\docType{package}
+\name{joinet-package}
+\alias{joinet-package}
+\title{Multivariate Elastic Net Regression}
+\description{
+The R package \code{joinet} implements multivariate
+ridge and lasso regression using stacked generalisation.
+This multivariate regression typically outperforms
+univariate regression at predicting correlated outcomes.
+It provides predictive and interpretable models
+in high-dimensional settings.
+}
+\details{
+Use function \code{\link{joinet}} for model fitting.
+Type \code{library(joinet)} and then \code{?joinet} or
+\code{help("joinet)"} to open its help file.
+
+See the vignette for further examples.
+Type \code{vignette("joinet")} or \code{browseVignettes("joinet")}
+to open the vignette.
+}
+\examples{
+#--- data simulation ---
+n <- 50; p <- 100; q <- 3
+X <- matrix(rnorm(n*p),nrow=n,ncol=p)
+Y <- replicate(n=q,expr=rnorm(n=n,mean=rowSums(X[,1:5])))
+# n samples, p inputs, q outputs
+
+#--- model fitting ---
+object <- joinet(Y=Y,X=X)
+# slot "base": univariate
+# slot "meta": multivariate
+
+#--- make predictions ---
+y_hat <- predict(object,newx=X)
+# n x q matrix "base": univariate
+# n x q matrix "meta": multivariate 
+
+#--- extract coefficients ---
+coef <- coef(object)
+# effects of inputs on outputs
+# q vector "alpha": intercepts
+# p x q matrix "beta": slopes
+
+#--- model comparison ---
+loss <- cv.joinet(Y=Y,X=X)
+# cross-validated loss
+# row "base": univariate
+# row "meta": multivariate
+
+}
+\references{
+Armin Rauschenberger and Enrico Glaab (2019).
+"joinet: predicting correlated outcomes jointly to improve clinical prognosis".
+\emph{Manuscript in preparation}.
+
+\email{armin.rauschenberger@uni.lu}
+}
+\keyword{documentation}

man/joinet.Rd

@@ -2,7 +2,6 @@
 % Please edit documentation in R/functions.R
 \name{joinet}
 \alias{joinet}
-\alias{joinet-package}
 \title{Multivariate Elastic Net Regression}
 \usage{
 joinet(Y, X, family = "gaussian", nfolds = 10, foldid = NULL,