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Commit 1d397058 authored by Armin Rauschenberger's avatar Armin Rauschenberger
Browse files

automation

parent 8f88fd0b
......@@ -12,5 +12,5 @@ License: GPL-3
LazyData: true
Language: en-GB
RoxygenNote: 6.1.1
URL: https://github.com/rauschenberger/stanet
BugReports: https://github.com/rauschenberger/stanet/issues
URL: https://github.com/rauschenberger/mixnet
BugReports: https://github.com/rauschenberger/mixnet/issues
......@@ -3,5 +3,6 @@
S3method(coef,mixnet)
S3method(predict,mixnet)
S3method(weights,mixnet)
export(cv.mixnet)
export(mixnet)
importFrom(stats,weights)
......@@ -2,6 +2,7 @@
#--- Main function -------------------------------------------------------------
#' @export
#' @aliases mixnet-package
#' @title
#' Multivariate Elastic Net Regression
#'
......@@ -76,6 +77,9 @@ mixnet <- function(Y,X,family="gaussian",nfolds=10,foldid=NULL,type.measure="dev
# family <- "gaussian"; nfolds <- 10; foldid <- NULL; type.measure <- "deviance"
#--- checks ---
Y <- as.matrix(Y)
X <- as.matrix(X)
cornet:::.check(x=Y,type="matrix",miss=TRUE)
if(any(stats::cor(Y,use="pairwise.complete.obs")<0,na.rm=TRUE)){warning("Negative correlation!",call.=FALSE)}
cornet:::.check(x=X,type="matrix")
......@@ -209,7 +213,7 @@ mixnet <- function(Y,X,family="gaussian",nfolds=10,foldid=NULL,type.measure="dev
#' @export
#' @title
#' Makes Predictions
#' Make Predictions
#'
#' @description
#' Predicts outcome from features with stacked model.
......@@ -230,8 +234,9 @@ mixnet <- function(Y,X,family="gaussian",nfolds=10,foldid=NULL,type.measure="dev
#'
#' @examples
#' n <- 30; q <- 2; p <- 20
#' Y <- matrix(rnorm(n*q),nrow=n,ncol=q)
#' #Y <- matrix(rnorm(n*q),nrow=n,ncol=q)
#' Y <- matrix(rbinom(n=n*q,size=1,prob=0.5),nrow=n,ncol=q)
#' #Y <- matrix(rpois(n=n*q,lambda=4),nrow=n,ncol=q)
#' X <- matrix(rnorm(n*p),nrow=n,ncol=p)
#' object <- mixnet(Y=Y,X=X,family="binomial")
#' y_hat <- predict(object,newx=X)
......@@ -241,6 +246,7 @@ predict.mixnet <- function(object,newx,type="response",...){
x <- object; rm(object)
newx <- as.matrix(newx)
cornet:::.check(x=newx,type="matrix")
q <- length(x$base)
......@@ -282,7 +288,8 @@ predict.mixnet <- function(object,newx,type="response",...){
#'
#' @description
#' Extracts pooled coefficients.
#' (The meta learners weights the coefficients from the base learners.)
#' (The meta learners linearly combines
#' the coefficients from the base learners.)
#'
#' @param object
#' \link[mixnet]{mixnet} object
......@@ -356,7 +363,6 @@ coef.mixnet <- function(object,...){
#' object <- mixnet(Y=Y,X=X)
#' weights(object)
#'
# object <- mixnet(Y=Y,X=X)
weights.mixnet <- function(object,...){
if(length(list(...))!=0){warning("Ignoring argument.",call.=FALSE)}
x <- object$meta
......@@ -373,15 +379,7 @@ print.mixnet <- function(x,...){
#--- Manuscript functions ------------------------------------------------------
# @param spls
# sparse partial least squares (logical)
# @param mnorm
# multivariate normal regression (logical)
# @param mrce
# multivariate regression with covariance estimation (logical)
#' @export
#' @title
#' Model comparison
#'
......@@ -408,31 +406,20 @@ print.mixnet <- function(x,...){
#' between \eqn{1} and \code{nfolds.int};
#' or \code{NULL}
#'
#' @param mnorm
#' multivariate normal regression\strong{:}
#' logical
#'
#' @param spls
#' sparse partial least squares\strong{:}
#' logical
#'
#' @param sier
#' high-dimensional multivariate regression\strong{:}
#' logical
#'
#' @param mrce
#' multivariate regression with covariance estimation\strong{:}
#' logical
#' @param mnorm,spls,sier,mrce
#' experimental arguments\strong{:}
#' logical (install packages \code{spls}, \code{SiER}, or \code{MRCE})
#'
#' @param ...
#' further arguments passed to \code{\link[glmnet]{glmnet}} and \code{\link[glmnet]{cv.glmnet}}
#'
#' @examples
#' NA
#' n <- 40; q <- 2; p <- 20
#' Y <- matrix(rnorm(n*q),nrow=n,ncol=q)
#' X <- matrix(rnorm(n*p),nrow=n,ncol=p)
#' cv.mixnet(Y=Y,X=X)
#'
compare <- 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,...){
# family <- "gaussian"; nfolds <- 5; foldid <- NULL; type.measure <- "deviance"; alpha.base=1;alpha.meta=0;spls=FALSE;mnorm=FALSE;sier=FALSE;mrce=FALSE
cv.mixnet <- 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,...){
n <- nrow(Y)
q <- ncol(Y)
......@@ -482,6 +469,7 @@ compare <- function(Y,X,family="gaussian",nfolds.ext=5,nfolds.int=10,foldid.ext=
x1 <- X1[,cond]
y0 <- apply(X=Y0,MARGIN=2,FUN=function(x) ifelse(is.na(x),sample(x[!is.na(x)],size=1),x))
all(Y0==y0,na.rm=TRUE)
if(mnorm){
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")
......
......@@ -9,10 +9,10 @@ authors:
home:
links:
- text: "Download package"
href: https://github.com/rauschenberger/stanet
href: https://github.com/rauschenberger/mixnet
navbar:
title: "stanet"
title: "mixnet"
left:
- text: "functions"
href: reference/index.html
......@@ -24,16 +24,17 @@ navbar:
href: news/index.html
right:
- icon: fa-github
href: https://github.com/rauschenberger/stanet
href: https://github.com/rauschenberger/mixnet
- icon: fa-download
href: https://cran.r-project.org/package=stanet
href: https://cran.r-project.org/package=mixnet
reference:
- title: "User functions"
contents:
- stacker
- predict.stacker
- coef.stacker
- weights.stacker
- mixnet
- predict.mixnet
- coef.mixnet
- weights.mixnet
- title: "Internal functions"
contents:
- cv.mixnet
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......@@ -22,14 +22,15 @@
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<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">mixnet</a>
<span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.0.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
</span>
</div>
......@@ -50,13 +51,13 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/rauschenberger/stanet">
<a href="https://github.com/rauschenberger/mixnet">
<span class="fa fa-github"></span>
</a>
</li>
<li>
<a href="https://cran.r-project.org/package=stanet">
<a href="https://cran.r-project.org/package=mixnet">
<span class="fa fa-download"></span>
</a>
......@@ -76,7 +77,7 @@
<h1>Stacked Elastic Net</h1>
<small class="dont-index">Source: <a href="https://github.com/rauschenberger/stanet/blob/master/vignettes/article.Rmd"><code>vignettes/article.Rmd</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/rauschenberger/mixnet/blob/master/vignettes/article.Rmd"><code>vignettes/article.Rmd</code></a></small>
<div class="hidden name"><code>article.Rmd</code></div>
</div>
......@@ -109,9 +110,8 @@
</div>
<div class="pkgdown">
<p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
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</footer>
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......
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......@@ -9,17 +9,17 @@
<title>Articles • mixnet</title>
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......@@ -35,7 +35,8 @@
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mixnet</a>
<span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.0.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
</span>
</div>
......@@ -80,13 +82,13 @@
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/rauschenberger/stanet">
<a href="https://github.com/rauschenberger/mixnet">
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</a>
</li>
<li>
<a href="https://cran.r-project.org/package=stanet">
<a href="https://cran.r-project.org/package=mixnet">
<span class="fa fa-download"></span>
</a>
......@@ -124,9 +126,8 @@
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......@@ -50,13 +51,13 @@
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......@@ -76,7 +77,7 @@
<h1>Multivariate Elastic Net</h1>
<small class="dont-index">Source: <a href="https://github.com/rauschenberger/stanet/blob/master/vignettes/vignette.Rmd"><code>vignettes/vignette.Rmd</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/rauschenberger/mixnet/blob/master/vignettes/vignette.Rmd"><code>vignettes/vignette.Rmd</code></a></small>
<div class="hidden name"><code>vignette.Rmd</code></div>
</div>
......@@ -87,11 +88,23 @@
<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=mixnet">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">install.packages</span>(<span class="st">"mixnet"</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"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"mixnet"</span>)</a></code></pre></div>
<p>or the latest development version from <a href="https://github.com/rauschenberger/mixnet">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="http://www.rdocumentation.org/packages/devtools/topics/reexports">install_github</a></span>(<span class="st">"rauschenberger/mixnet"</span>)</a></code></pre></div>
<p>Armin Rauschenberger and Enrico Glaab (2019). “Improved elastic net regression through stacked generalisation”. <em>Manuscript in preparation.</em></p>
<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/mixnet"</span>)</a></code></pre></div>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1"><span class="co">#install.packages("plsgenomics")</span></a>
<a class="sourceLine" id="cb3-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/data">data</a></span>(Ecoli,<span class="dt">package=</span><span class="st">"plsgenomics"</span>)</a>
<a class="sourceLine" id="cb3-3" title="3">X &lt;-<span class="st"> </span>Ecoli<span class="op">$</span>CONNECdata</a>
<a class="sourceLine" id="cb3-4" title="4">Y &lt;-<span class="st"> </span>Ecoli<span class="op">$</span>GEdata</a>
<a class="sourceLine" id="cb3-5" title="5">loss &lt;-<span class="st"> </span>mixnet<span class="op">:::</span><span class="kw"><a href="../reference/cv.mixnet.html">cv.mixnet</a></span>(<span class="dt">Y=</span>Y,<span class="dt">X=</span>X)</a></code></pre></div>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="co">#install.packages("BiocManager")</span></a>
<a class="sourceLine" id="cb4-2" title="2"><span class="co">#BiocManager::install("mixOmics")</span></a>
<a class="sourceLine" id="cb4-3" title="3"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/data">data</a></span>(liver.toxicity,<span class="dt">package=</span><span class="st">"mixOmics"</span>)</a>
<a class="sourceLine" id="cb4-4" title="4">X &lt;-<span class="st"> </span>liver.toxicity<span class="op">$</span>gene</a>
<a class="sourceLine" id="cb4-5" title="5">Y &lt;-<span class="st"> </span>liver.toxicity<span class="op">$</span>clinic</a>
<a class="sourceLine" id="cb4-6" title="6">Y<span class="op">$</span>Cholesterol.mg.dL. &lt;-<span class="st"> </span><span class="op">-</span>Y<span class="op">$</span>Cholesterol.mg.dL.</a>
<a class="sourceLine" id="cb4-7" title="7">loss &lt;-<span class="st"> </span>mixnet<span class="op">:::</span><span class="kw"><a href="../reference/cv.mixnet.html">cv.mixnet</a></span>(<span class="dt">Y=</span>Y,<span class="dt">X=</span>X)</a></code></pre></div>
<p>Armin Rauschenberger and Enrico Glaab (2019). “Multivariate regression through stacked generalisation”. <em>Manuscript in preparation.</em></p>
</div>
</div>
......@@ -113,9 +126,8 @@
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......@@ -35,7 +35,8 @@
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<span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.0.1</span>
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</span>
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......@@ -80,13 +82,13 @@
<ul class="nav navbar-nav navbar-right">
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......@@ -124,9 +126,8 @@
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</span>
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......@@ -50,13 +51,13 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/rauschenberger/stanet">
<a href="https://github.com/rauschenberger/mixnet">
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</a>
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<li>
<a href="https://cran.r-project.org/package=stanet">
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<span class="fa fa-download"></span>
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......@@ -87,10 +88,10 @@
<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=stanet">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">install.packages</span>(<span class="st">"stanet"</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"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"stanet"</span>)</a></code></pre></div>
<p>or the latest development version from <a href="https://github.com/rauschenberger/stanet">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="http://www.rdocumentation.org/packages/devtools/topics/reexports">install_github</a></span>(<span class="st">"rauschenberger/stanet"</span>)</a></code></pre></div>
<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/stanet"</span>)</a></code></pre></div>
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<div id="reference" class="section level2">
<h2 class="hasAnchor">
......@@ -105,11 +106,11 @@
<ul class="list-unstyled">
<li>Download from CRAN at <br><a href="https://cloud.r-project.org/package=mixnet">https://​cloud.r-project.org/​package=mixnet</a>
</li>