competing models

448ee92c · Armin Rauschenberger · ffa77bbb · 448ee92c · 448ee92c · 448ee92c
Commit 448ee92c authored Oct 02, 2020 by Armin Rauschenberger
27 changed files
--- a/DESCRIPTION
+++ b/DESCRIPTION
 Package: joinet
-Version: 0.0.4
+Version: 0.0.5
 Title: Multivariate Elastic Net Regression
 Description: Implements high-dimensional multivariate regression by stacked generalisation (Wolpert 1992 <doi:10.1016/S0893-6080(05)80023-1>). For positively correlated outcomes, a single multivariate regression is typically more predictive than multiple univariate regressions. Includes functions for model fitting, extracting coefficients, outcome prediction, and performance measurement.
 Depends: R (>= 3.0.0)
@@ -11,6 +11,6 @@ VignetteBuilder: knitr
 License: GPL-3
 LazyData: true
 Language: en-GB
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.1
 URL: https://github.com/rauschenberger/joinet
 BugReports: https://github.com/rauschenberger/joinet/issues
--- a/NEWS.md
+++ b/NEWS.md

+## joinet 0.0.5 (2020-10-02)
+
+* updated documentation
+
 ## joinet 0.0.4 (2020-05-06)

 * added competing models

--- a/R/functions.R
+++ b/R/functions.R
@@ -53,9 +53,8 @@
 #' further arguments passed to \code{\link[glmnet]{glmnet}}
 #' 
 #' @references 
-#' Armin Rauschenberger, Enrico Glaab (2019)
-#' "joinet: predicting correlated outcomes jointly
-#' to improve clinical prognosis"
+#' Armin Rauschenberger, Enrico Glaab (2020)
+#' "Predicting correlated outcomes from molecular data"
 #' \emph{Manuscript in preparation}.
 #' 
 #' @details
@@ -472,6 +471,10 @@ print.joinet <- function(x,...){
 #' @param cvpred
 #' return cross-validated predicitions: logical
 #' 
+#' @param times
+#' measure computation time\strong{:}
+#' logical
+#' 
 #' @param ...
 #' further arguments passed to \code{\link[glmnet]{glmnet}}
 #' and \code{\link[glmnet]{cv.glmnet}}
@@ -684,7 +687,8 @@ cv.joinet <- function(Y,X,family="gaussian",nfolds.ext=5,nfolds.int=10,foldid.ex
      # tune nprune (use default nk)!
      }
      
-      pred$mars[foldid.ext==i,] <- earth:::predict.earth(object=object,newdata=X1,type="response")
+      #pred$mars[foldid.ext==i,] <- earth:::predict.earth(object=object,newdata=X1,type="response") # original
+      pred$mars[foldid.ext==i,] <- stats::predict(object=object,newdata=X1,type="response") # trial
      end <- Sys.time()
      time$mars <- as.numeric(difftime(end,start,units="secs"))
    }
@@ -784,7 +788,8 @@ cv.joinet <- function(Y,X,family="gaussian",nfolds.ext=5,nfolds.int=10,foldid.ex
      object <- mcen::cv.mcen(x=X0,y=y0,family=type,folds=foldid,ky=1,
                              gamma_y=seq(from=0.1,to=5.1,by=1),ndelta=5)
      # TEMPORARY gamma_y=seq(from=0.1,to=5.1,length.out=3) and ndelta=3 (for speed-up)
-      temp <- mcen:::predict.cv.mcen(object=object,newx=X1)
+      #temp <- mcen:::predict.cv.mcen(object=object,newx=X1) # original
+      temp <- stats::predict(object=object,newx=X1) # trial
      pred$mcen[foldid.ext==i,] <- as.matrix(temp)
      # single cluster (ky=1) due to setting and error
      end <- Sys.time()
@@ -835,7 +840,8 @@ cv.joinet <- function(Y,X,family="gaussian",nfolds.ext=5,nfolds.int=10,foldid.ex
      #--- manual tuning end ----
      #--------------------------
      MTL <- RMTL::MTL(X=X0l,Y=y0l,type=type,Lam1=Lam1,Lam2=Lam2)
-      temp <- RMTL:::predict.MTL(object=MTL,newX=X1l)
+      #temp <- RMTL:::predict.MTL(object=MTL,newX=X1l) # original
+      temp <- stats::predict(object=MTL,newX=X1l)
      pred$rmtl[foldid.ext==i,] <- do.call(what="cbind",args=temp)
      end <- Sys.time()
      time$rmtl <- as.numeric(difftime(end,start,units="secs"))
@@ -901,25 +907,25 @@ cv.joinet <- function(Y,X,family="gaussian",nfolds.ext=5,nfolds.int=10,foldid.ex
    # --- development ---
    
    if(FALSE){
-      # --- MLPUGS --- (binary outcome only)
-      X0f <- as.data.frame(X0)
-      y0f <- as.data.frame(y0)
-      X1f <- as.data.frame(X1)
-      object <- MLPUGS::ecc(x=X0f,y=y0f,.f=randomForest::randomForest)
-      pred_ecc <- predict(object,newdata=X1f,n.iters=300,burn.in=100,thin=2,
-          .f = function(rF,newdata){randomForest:::predict.randomForest(rF, newdata, type = "prob")})
-      pred$ecc[foldid.ext==i,] <- summary(pred_ecc,type="prob")
-      # --- MSGLasso --- (many user inputs)
-      MSGLasso::MSGLasso.cv(X=X0,Y=Y0)
-      # --- PMA --- (not for prediction?)
-      # --- MSP --- (not for hd data?)
-      object <- MBSP::mbsp.tpbn(X=X0,Y=Y0)
-      X1 %*% object$B # adjust for intercept
-      # --- bgsmtr --- (for SNPs only?)
-      temp <- bgsmtr::bgsmtr(X=t(X0),Y=t(Y0),group=rep(1,times=ncol(X0)))
-      # --- MGLM --- (for multinomial data only?)
-      MGLM::MGLMsparsereg.fit()
-      MGLM::MGLMtune()
+      ## --- MLPUGS --- (binary outcome only)
+      #X0f <- as.data.frame(X0)
+      #y0f <- as.data.frame(y0)
+      #X1f <- as.data.frame(X1)
+      #object <- MLPUGS::ecc(x=X0f,y=y0f,.f=randomForest::randomForest)
+      #pred_ecc <- predict(object,newdata=X1f,n.iters=300,burn.in=100,thin=2,
+      #    .f = function(rF,newdata){randomForest:::predict.randomForest(rF, newdata, type = "prob")})
+      #pred$ecc[foldid.ext==i,] <- summary(pred_ecc,type="prob")
+      ## --- MSGLasso --- (many user inputs)
+      #MSGLasso::MSGLasso.cv(X=X0,Y=Y0)
+      ## --- PMA --- (not for prediction?)
+      ## --- MSP --- (not for hd data?)
+      #object <- MBSP::mbsp.tpbn(X=X0,Y=Y0)
+      #X1 %*% object$B # adjust for intercept
+      ## --- bgsmtr --- (for SNPs only?)
+      #temp <- bgsmtr::bgsmtr(X=t(X0),Y=t(Y0),group=rep(1,times=ncol(X0)))
+      ## --- MGLM --- (for multinomial data only?)
+      #MGLM::MGLMsparsereg.fit()
+      #MGLM::MGLMtune()
    }
    
    pred$none[foldid.ext==i,] <- matrix(colMeans(Y0,na.rm=TRUE),nrow=sum(foldid.ext==i),ncol=ncol(Y0),byrow=TRUE)
@@ -950,8 +956,6 @@ cv.joinet <- function(Y,X,family="gaussian",nfolds.ext=5,nfolds.int=10,foldid.ex
  return(loss)
 }

-
-
 plot.matrix <- function (X, margin = 0, labels = TRUE, las = 1, cex = 1, range = NULL, cutoff = 0, digits=2) {
  #margin <- 0; labels <- TRUE; las <- 1; cex <- 1; range <- NULL; cutoff <- 0; digits <- 2
  

--- a/R/pkgname.R
+++ b/R/pkgname.R
@@ -24,8 +24,8 @@
 #' to open the vignette.
 #' 
 #' @references
-#' Armin Rauschenberger and Enrico Glaab (2019).
-#' "joinet: predicting correlated outcomes jointly to improve clinical prognosis".
+#' Armin Rauschenberger and Enrico Glaab (2020).
+#' "Predicting correlated outcomes from molecular data".
 #' \emph{Manuscript in preparation}.
 #' 
 #' \email{armin.rauschenberger@uni.lu}

--- a/README.Rmd
+++ b/README.Rmd
@@ -40,7 +40,7 @@ devtools::install_github("rauschenberger/joinet")

 ## Reference

-Armin Rauschenberger and Enrico Glaab (2019). "Predicting correlated outcomes jointly to improve clinical prognosis". *Manuscript in preparation.*
+Armin Rauschenberger and Enrico Glaab (2020). "Predicting correlated outcomes from molecular data". *Manuscript in preparation.*

 [![CRAN version](https://www.r-pkg.org/badges/version/joinet)](https://CRAN.R-project.org/package=joinet)
 [![CRAN RStudio mirror downloads](https://cranlogs.r-pkg.org/badges/joinet)](https://CRAN.R-project.org/package=joinet)

--- a/README.md
+++ b/README.md
@@ -33,9 +33,8 @@ devtools::install_github("rauschenberger/joinet")

 ## Reference

-Armin Rauschenberger and Enrico Glaab (2019). “Predicting correlated
-outcomes jointly to improve clinical prognosis”. *Manuscript in
-preparation.*
+Armin Rauschenberger and Enrico Glaab (2020). “Predicting correlated
+outcomes from molecular data”. *Manuscript in preparation.*

 [![CRAN
 version](https://www.r-pkg.org/badges/version/joinet)](https://CRAN.R-project.org/package=joinet)

--- a/docs/404.html
+++ b/docs/404.html
@@ -71,7 +71,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="index.html">joinet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.5</span>
      </span>
    </div>


--- a/docs/articles/article.html
+++ b/docs/articles/article.html
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+<title>Multivariate Elastic Net Regression • joinet</title>
+<!-- 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/3.4.1/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 --><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/5.12.1/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="Multivariate Elastic Net Regression">
+<meta property="og:description" content="joinet">
+<!-- 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/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+</head>
+<body data-spy="scroll" data-target="#toc">
+    <div class="container template-article">
+      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
+  <div class="container">
+    <div class="navbar-header">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+      </button>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">joinet</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.5</span>
+      </span>
+    </div>
+
+    <div id="navbar" class="navbar-collapse collapse">
+      <ul class="nav navbar-nav">
+<li>
+  <a href="../reference/index.html">functions</a>
+</li>
+<li>
+  <a href="../articles/joinet.html">vignette</a>
+</li>
+<li>
+  <a href="../articles/article.html">article</a>
+</li>
+<li>
+  <a href="../news/index.html">news</a>
+</li>
+      </ul>
+<ul class="nav navbar-nav navbar-right">
+<li>
+  <a href="https://github.com/rauschenberger/joinet">
+    <span class="fa fa-github"></span>
+     
+  </a>
+</li>
+<li>
+  <a href="https://cran.r-project.org/package=joinet">
+    <span class="fa fa-download"></span>
+     
+  </a>
+</li>
+      </ul>
+</div>
+<!--/.nav-collapse -->
+  </div>
+<!--/.container -->
+</div>
+<!--/.navbar -->
+
+      
+
+      </header><div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header toc-ignore">
+      <h1 data-toc-skip>Multivariate Elastic Net Regression</h1>
+            
+      
+      <small class="dont-index">Source: <a href="https://github.com/rauschenberger/joinet/blob/master/vignettes/article.Rmd"><code>vignettes/article.Rmd</code></a></small>
+      <div class="hidden name"><code>article.Rmd</code></div>
+
+    </div>
+
+    
+    
+<p>The <code>joinet</code> manuscript is in preparation. Click <a href="https://CRAN.R-project.org/package=joinet">here</a> for the R package.</p>
+<div id="reference" class="section level2">
+<h2 class="hasAnchor">
+<a href="#reference" class="anchor"></a>Reference</h2>
+<p>Armin Rauschenberger and Enrico Glaab (2020). “Predicting correlated outcomes from molecular data”. <em>Manuscript in preparation.</em></p>
+</div>
+  </div>
+
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+
+        <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2>
+    </nav>
+</div>
+
+</div>
+
+
+
+      <footer><div class="copyright">
+  <p>Developed by <a href="https://rauschenberger.github.io">Armin Rauschenberger</a>.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+</div>
+
+      </footer>
+</div>
+
+  
+
+
+  </body>
+</html>
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+  <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Articles • joinet</title>
+
+
+<!-- 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/3.4.1/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 -->
+<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/5.12.1/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="Articles" />
+
+
+
+
+<!-- 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/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+
+  </head>
+
+  <body data-spy="scroll" data-target="#toc">
+    <div class="container template-article-index">
+      <header>
+      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+  <div class="container">
+    <div class="navbar-header">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+      </button>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">joinet</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.5</span>
+      </span>
+    </div>
+
+    <div id="navbar" class="navbar-collapse collapse">
+      <ul class="nav navbar-nav">
+        <li>
+  <a href="../reference/index.html">functions</a>
+</li>
+<li>
+  <a href="../articles/joinet.html">vignette</a>
+</li>
+<li>
+  <a href="../articles/article.html">article</a>
+</li>
+<li>
+  <a href="../news/index.html">news</a>
+</li>
+      </ul>
+      <ul class="nav navbar-nav navbar-right">
+        <li>
+  <a href="https://github.com/rauschenberger/joinet">
+    <span class="fa fa-github"></span>
+     
+  </a>
+</li>
+<li>
+  <a href="https://cran.r-project.org/package=joinet">
+    <span class="fa fa-download"></span>
+     
+  </a>
+</li>
+      </ul>
+      
+    </div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+
+      </header>
+
+<div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+      <h1>Articles</h1>
+    </div>
+
+    <div class="section ">
+      <h3>All vignettes</h3>
+      <p class="section-desc"></p>
+
+      <dl>
+        <dt><a href="article.html">Multivariate Elastic Net Regression</a></dt>
+        <dd></dt>
+        <dt><a href="joinet.html">Multivariate Elastic Net Regression</a></dt>
+        <dd></dt>
+      </dl>
+    </div>
+  </div>
+</div>
+
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by <a href='https://rauschenberger.github.io'>Armin Rauschenberger</a>.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+</div>
+
+      </footer>
+   </div>
+
+  
+
+
+  </body>
+</html>
+
+
--- a/docs/articles/joinet.html
+++ b/docs/articles/joinet.html
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -71,7 +71,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="index.html">joinet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.5</span>
      </span>
    </div>


--- a/docs/index.html
+++ b/docs/index.html
@@ -31,7 +31,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="index.html">joinet</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.5</span>
      </span>
    </div>

@@ -94,7 +94,7 @@
 <div id="reference" class="section level2">
 <h2 class="hasAnchor">
 <a href="#reference" class="anchor"></a>Reference</h2>
-<p>Armin Rauschenberger and Enrico Glaab (2019). “Predicting correlated outcomes jointly to improve clinical prognosis”. <em>Manuscript in preparation.</em></p>
+<p>Armin Rauschenberger and Enrico Glaab (2020). “Predicting correlated outcomes from molecular data”. <em>Manuscript in preparation.</em></p>
 <p><a href="https://CRAN.R-project.org/package=joinet"><img src="https://www.r-pkg.org/badges/version/joinet" alt="CRAN version"></a> <a href="https://CRAN.R-project.org/package=joinet"><img src="https://cranlogs.r-pkg.org/badges/joinet" alt="CRAN RStudio mirror downloads"></a> <a href="https://CRAN.R-project.org/package=joinet"><img src="https://cranlogs.r-pkg.org/badges/grand-total/joinet" alt="Total CRAN downloads"></a></p>
 </div>


--- a/docs/news/index.html
+++ b/docs/news/index.html
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+  <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Changelog • joinet</title>
+
+
+<!-- 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/3.4.1/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 -->
+<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/5.12.1/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="Changelog" />
+
+
+
+
+<!-- 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/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+
+  </head>
+
+  <body data-spy="scroll" data-target="#toc">
+    <div class="container template-news">
+      <header>
+      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+  <div class="container">
+    <div class="navbar-header">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+      </button>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">joinet</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.5</span>
+      </span>
+    </div>
+
+    <div id="navbar" class="navbar-collapse collapse">
+      <ul class="nav navbar-nav">
+        <li>
+  <a href="../reference/index.html">functions</a>
+</li>
+<li>
+  <a href="../articles/joinet.html">vignette</a>
+</li>
+<li>
+  <a href="../articles/article.html">article</a>
+</li>
+<li>
+  <a href="../news/index.html">news</a>
+</li>
+      </ul>
+      <ul class="nav navbar-nav navbar-right">
+        <li>
+  <a href="https://github.com/rauschenberger/joinet">
+    <span class="fa fa-github"></span>
+     
+  </a>
+</li>
+<li>
+  <a href="https://cran.r-project.org/package=joinet">
+    <span class="fa fa-download"></span>
+     
+  </a>
+</li>
+      </ul>
+      
+    </div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+
+      </header>
+
+<div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+      <h1 data-toc-skip>Changelog <small></small></h1>
+      <small>Source: <a href='https://github.com/rauschenberger/joinet/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
+    </div>
+
+    <div id="joinet-005-2020-10-02" class="section level2">
+<h2 class="hasAnchor">
+<a href="#joinet-005-2020-10-02" class="anchor"></a>joinet 0.0.5 (2020-10-02)</h2>
+<ul>
+<li>updated documentation</li>
+</ul>
+</div>
+    <div id="joinet-004-2020-05-06" class="section level2">
+<h2 class="hasAnchor">
+<a href="#joinet-004-2020-05-06" class="anchor"></a>joinet 0.0.4 (2020-05-06)</h2>
+<ul>
+<li>added competing models</li>
+</ul>
+</div>
+    <div id="joinet-003-2019-11-12" class="section level2">
+<h2 class="hasAnchor">
+<a href="#joinet-003-2019-11-12" class="anchor"></a>joinet 0.0.3 (2019-11-12)</h2>
+<ul>
+<li>changed glmnet exports</li>
+</ul>
+</div>
+    <div id="joinet-002-2019-08-08" class="section level2">
+<h2 class="hasAnchor">
+<a href="#joinet-002-2019-08-08" class="anchor"></a>joinet 0.0.2 (2019-08-08)</h2>
+<ul>
+<li>performance comparison</li>
+</ul>
+</div>
+    <div id="joinet-001-2019-08-03" class="section level2">
+<h2 class="hasAnchor">
+<a href="#joinet-001-2019-08-03" class="anchor"></a>joinet 0.0.1 (2019-08-03)</h2>
+<ul>
+<li>first submission</li>
+</ul>
+</div>
+  </div>
+
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">