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Commit d4dfc9da authored by Armin Rauschenberger's avatar Armin Rauschenberger
Browse files

automation

parent 1740863b
...@@ -205,7 +205,7 @@ joinet <- function(Y,X,family="gaussian",nfolds=10,foldid=NULL,type.measure="dev ...@@ -205,7 +205,7 @@ joinet <- function(Y,X,family="gaussian",nfolds=10,foldid=NULL,type.measure="dev
} }
.mean.function <- function(x,family){ .mean.function <- function(x,family){
if(family=="gaussian"){ if(family %in% c("gaussian","cox")){
return(x) return(x)
} else if(family=="binomial"){ } else if(family=="binomial"){
return(1/(1+exp(-x))) return(1/(1+exp(-x)))
...@@ -217,7 +217,7 @@ joinet <- function(Y,X,family="gaussian",nfolds=10,foldid=NULL,type.measure="dev ...@@ -217,7 +217,7 @@ joinet <- function(Y,X,family="gaussian",nfolds=10,foldid=NULL,type.measure="dev
} }
.link.function <- function(x,family){ .link.function <- function(x,family){
if(family=="gaussian"){ if(family %in% c("gaussian","cox")){
return(x) return(x)
} else if(family=="binomial"){ } else if(family=="binomial"){
if(any(x<0|x>1)){stop("Invalid!",call.=FALSE)} if(any(x<0|x>1)){stop("Invalid!",call.=FALSE)}
...@@ -262,7 +262,8 @@ joinet <- function(Y,X,family="gaussian",nfolds=10,foldid=NULL,type.measure="dev ...@@ -262,7 +262,8 @@ joinet <- function(Y,X,family="gaussian",nfolds=10,foldid=NULL,type.measure="dev
#' n <- 50; p <- 100; q <- 3 #' n <- 50; p <- 100; q <- 3
#' X <- matrix(rnorm(n*p),nrow=n,ncol=p) #' X <- matrix(rnorm(n*p),nrow=n,ncol=p)
#' Y <- replicate(n=q,expr=rnorm(n=n,mean=rowSums(X[,1:5]))) #' Y <- replicate(n=q,expr=rnorm(n=n,mean=rowSums(X[,1:5])))
#' object <- joinet(Y=Y,X=X) #' Y[,1] <- 1*(Y[,1]>median(Y[,1]))
#' object <- joinet(Y=Y,X=X,family=c("binomial","gaussian","gaussian"))
#' predict(object,newx=X) #' predict(object,newx=X)
#' #'
predict.joinet <- function(object,newx,type="response",...){ predict.joinet <- function(object,newx,type="response",...){
...@@ -279,8 +280,8 @@ predict.joinet <- function(object,newx,type="response",...){ ...@@ -279,8 +280,8 @@ predict.joinet <- function(object,newx,type="response",...){
# base learners # base learners
for(i in seq_len(q)){ for(i in seq_len(q)){
#base[,i] <- as.numeric(stats::predict(object=x$base[[i]]$glmnet.fit,newx=newx,s=x$base[[i]]$lambda.min,type="link")) base[,i] <- as.numeric(stats::predict(object=x$base[[i]]$glmnet.fit,newx=newx,s=x$base[[i]]$lambda.min,type="link"))
base[,i] <- as.numeric(glmnet::predict.cv.glmnet(object=x$base[[i]],newx=newx,s="lambda.min",type="link")) #base[,i] <- as.numeric(glmnet:::predict.cv.glmnet(object=x$base[[i]],newx=newx,s="lambda.min",type="link"))
# check whether fine for "binomial" family # check whether fine for "binomial" family
} }
...@@ -340,7 +341,7 @@ coef.joinet <- function(object,...){ ...@@ -340,7 +341,7 @@ coef.joinet <- function(object,...){
# base coefficients # base coefficients
base <- list() base <- list()
coef <- sapply(object$base,function(x) glmnet::coef.glmnet(object=x$glmnet.fit,s=x$lambda.min)) coef <- sapply(object$base,function(x) stats::coef(object=x$glmnet.fit,s=x$lambda.min))
base$alpha <- sapply(coef,function(x) x[1,]) base$alpha <- sapply(coef,function(x) x[1,])
base$beta <- sapply(coef,function(x) x[-1,]) base$beta <- sapply(coef,function(x) x[-1,])
names(base$alpha) <- colnames(base$beta) <- names(object$base) names(base$alpha) <- colnames(base$beta) <- names(object$base)
...@@ -405,7 +406,7 @@ coef.joinet <- function(object,...){ ...@@ -405,7 +406,7 @@ coef.joinet <- function(object,...){
weights.joinet <- function(object,...){ weights.joinet <- function(object,...){
if(length(list(...))!=0){warning("Ignoring argument.",call.=FALSE)} if(length(list(...))!=0){warning("Ignoring argument.",call.=FALSE)}
x <- object$meta x <- object$meta
coef <- lapply(object$meta,function(x) glmnet::coef.glmnet(object=x,s=x$lambda.min)) coef <- lapply(object$meta,function(x) stats::coef(object=x,s=x$lambda.min))
coef <- do.call(what="cbind",args=coef) coef <- do.call(what="cbind",args=coef)
coef <- as.matrix(coef) coef <- as.matrix(coef)
colnames(coef) <- names(object$meta) colnames(coef) <- names(object$meta)
...@@ -449,6 +450,9 @@ print.joinet <- function(x,...){ ...@@ -449,6 +450,9 @@ print.joinet <- function(x,...){
#' experimental arguments\strong{:} #' experimental arguments\strong{:}
#' logical (requires packages \code{spls}, \code{SiER}, or \code{MRCE}) #' logical (requires packages \code{spls}, \code{SiER}, or \code{MRCE})
#' #'
#' @param cvpred
#' return cross-validated predicition: logical
#'
#' @param ... #' @param ...
#' further arguments passed to \code{\link[glmnet]{glmnet}} #' further arguments passed to \code{\link[glmnet]{glmnet}}
#' and \code{\link[glmnet]{cv.glmnet}} #' and \code{\link[glmnet]{cv.glmnet}}
...@@ -504,7 +508,7 @@ print.joinet <- function(x,...){ ...@@ -504,7 +508,7 @@ print.joinet <- function(x,...){
#' set.seed(1) #' set.seed(1)
#' cv.joinet(Y=Y,X=X,alpha.base=0) # ridge} #' cv.joinet(Y=Y,X=X,alpha.base=0) # ridge}
#' #'
cv.joinet <- function(Y,X,family="gaussian",nfolds.ext=5,nfolds.int=10,foldid.ext=NULL,foldid.int=NULL,type.measure="deviance",alpha.base=1,alpha.meta=0,mnorm=FALSE,spls=FALSE,sier=FALSE,mrce=FALSE,...){ cv.joinet <- function(Y,X,family="gaussian",nfolds.ext=5,nfolds.int=10,foldid.ext=NULL,foldid.int=NULL,type.measure="deviance",alpha.base=1,alpha.meta=0,mnorm=FALSE,spls=FALSE,sier=FALSE,mrce=FALSE,cvpred=FALSE,...){
n <- nrow(Y) n <- nrow(Y)
q <- ncol(Y) q <- ncol(Y)
...@@ -557,7 +561,7 @@ cv.joinet <- function(Y,X,family="gaussian",nfolds.ext=5,nfolds.int=10,foldid.ex ...@@ -557,7 +561,7 @@ cv.joinet <- function(Y,X,family="gaussian",nfolds.ext=5,nfolds.int=10,foldid.ex
if(mnorm){ if(mnorm){
net <- glmnet::cv.glmnet(x=X0,y=y0,family="mgaussian",foldid=foldid,...) # ellipsis net <- glmnet::cv.glmnet(x=X0,y=y0,family="mgaussian",foldid=foldid,...) # ellipsis
pred$mnorm[foldid.ext==i,] <- glmnet::predict.cv.glmnet(object=net,newx=X1,s="lambda.min",type="response") pred$mnorm[foldid.ext==i,] <- stats::predict(object=net,newx=X1,s="lambda.min",type="response")
} }
if(spls){ if(spls){
cv.spls <- spls::cv.spls(x=x0,y=y0,fold=nfolds.int,K=seq_len(10), cv.spls <- spls::cv.spls(x=x0,y=y0,fold=nfolds.int,K=seq_len(10),
...@@ -595,5 +599,9 @@ cv.joinet <- function(Y,X,family="gaussian",nfolds.ext=5,nfolds.int=10,foldid.ex ...@@ -595,5 +599,9 @@ cv.joinet <- function(Y,X,family="gaussian",nfolds.ext=5,nfolds.int=10,foldid.ex
#fit <- joinet(Y=Y,X=X,family=family,type.measure=type.measure,alpha.base=alpha.base,alpha.meta=alpha.meta) # add ,... #fit <- joinet(Y=Y,X=X,family=family,type.measure=type.measure,alpha.base=alpha.base,alpha.meta=alpha.meta) # add ,...
#list <- list(loss=loss,fit=fit) #list <- list(loss=loss,fit=fit)
if(cvpred){
loss <- list(loss=loss,cvpred=pred$meta)
}
return(loss) return(loss)
} }
# Notes # Notes
Please accept ::: calls to "palasso" and "cornet", - Package runs without errors with palasso 0.0.6 (pending manual inspection).
as maintainer email changes for all packages. \ No newline at end of file
\ No newline at end of file
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...@@ -7,8 +7,9 @@ ...@@ -7,8 +7,9 @@
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...@@ -71,6 +72,7 @@ ...@@ -71,6 +72,7 @@
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...@@ -93,6 +95,7 @@ ...@@ -93,6 +95,7 @@
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<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> <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>
...@@ -44,6 +50,7 @@ ...@@ -44,6 +50,7 @@
<![endif]--> <![endif]-->
</head> </head>
<body> <body>
...@@ -79,7 +86,6 @@ ...@@ -79,7 +86,6 @@
<a href="../news/index.html">news</a> <a href="../news/index.html">news</a>
</li> </li>
</ul> </ul>
<ul class="nav navbar-nav navbar-right"> <ul class="nav navbar-nav navbar-right">
<li> <li>
<a href="https://github.com/rauschenberger/joinet"> <a href="https://github.com/rauschenberger/joinet">
...@@ -100,6 +106,7 @@ ...@@ -100,6 +106,7 @@
</div><!--/.navbar --> </div><!--/.navbar -->
</header> </header>
<div class="row"> <div class="row">
...@@ -120,19 +127,23 @@ ...@@ -120,19 +127,23 @@
</div> </div>
</div> </div>
<footer> <footer>
<div class="copyright"> <div class="copyright">
<p>Developed by <a href='https://rauschenberger.github.io'>Armin Rauschenberger</a>.</p> <p>Developed by <a href='https://rauschenberger.github.io'>Armin Rauschenberger</a>.</p>
</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="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div> </div>
</footer> </footer>
</div> </div>
</body> </body>
</html> </html>
This diff is collapsed.
...@@ -8,21 +8,25 @@ ...@@ -8,21 +8,25 @@
<title>Authors • joinet</title> <title>Authors • joinet</title>
<!-- jquery --> <!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap --> <!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" /> <link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/spacelab/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons --> <!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
<!-- clipboard.js --> <!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit --> <!-- headroom.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown --> <!-- pkgdown -->
<link href="pkgdown.css" rel="stylesheet"> <link href="pkgdown.css" rel="stylesheet">
...@@ -30,10 +34,12 @@ ...@@ -30,10 +34,12 @@
<meta property="og:title" content="Authors" /> <meta property="og:title" content="Authors" />
<!-- mathjax --> <!-- 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/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> <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>
...@@ -44,6 +50,7 @@ ...@@ -44,6 +50,7 @@
<![endif]--> <![endif]-->
</head> </head>
<body> <body>
...@@ -79,7 +86,6 @@ ...@@ -79,7 +86,6 @@
<a href="news/index.html">news</a> <a href="news/index.html">news</a>
</li> </li>
</ul> </ul>
<ul class="nav navbar-nav navbar-right"> <ul class="nav navbar-nav navbar-right">
<li> <li>
<a href="https://github.com/rauschenberger/joinet"> <a href="https://github.com/rauschenberger/joinet">
...@@ -100,6 +106,7 @@ ...@@ -100,6 +106,7 @@
</div><!--/.navbar --> </div><!--/.navbar -->
</header> </header>
<div class="row"> <div class="row">
...@@ -120,19 +127,23 @@ ...@@ -120,19 +127,23 @@
</div> </div>
<footer> <footer>
<div class="copyright">