[Depmix-commits] r196 - in trunk: R man

[noreply at r-forge.r-project.org]

Author: ingmarvisser
Date: 2008-06-30 11:41:27 +0200 (Mon, 30 Jun 2008)
New Revision: 196

Added:
   trunk/man/makeDepmix.Rd
Modified:
   trunk/R/responseGLM.R
   trunk/man/depmix-internal.Rd
Log:
Added help file for makeDepmix

Modified: trunk/R/responseGLM.R
===================================================================
--- trunk/R/responseGLM.R	2008-06-30 09:10:45 UTC (rev 195)
+++ trunk/R/responseGLM.R	2008-06-30 09:41:27 UTC (rev 196)
@@ -16,7 +16,7 @@
 
 setMethod("GLMresponse",
 	signature(formula="formula"),
-	function(formula,family=gaussian(),data,pstart=NULL,fixed=NULL,prob=TRUE, ...) {
+	function(formula,data=NULL,family=gaussian(),pstart=NULL,fixed=NULL,prob=TRUE, ...) {
 		call <- match.call()
 		mf <- match.call(expand.dots = FALSE)
 		m <- match(c("formula", "data"), names(mf), 0)
Modified: trunk/man/depmix-internal.Rd
===================================================================
--- trunk/man/depmix-internal.Rd	2008-06-30 09:10:45 UTC (rev 195)
+++ trunk/man/depmix-internal.Rd	2008-06-30 09:41:27 UTC (rev 196)
@@ -6,7 +6,6 @@
 \alias{logDens}
 \alias{lystig}
 
-\alias{makeDepmix}
 \alias{makeMix}
 \alias{makePriorModel}
 \alias{makeResponseModels}

Added: trunk/man/makeDepmix.Rd
===================================================================
--- trunk/man/makeDepmix.Rd	                        (rev 0)
+++ trunk/man/makeDepmix.Rd	2008-06-30 09:41:27 UTC (rev 196)
@@ -0,0 +1,131 @@
+
+\name{depmix}
+
+\docType{methods}
+
+\alias{makeDepmix}
+
+\title{Dependent Mixture Model Specifiction: the long way}
+
+\description{
+	
+	\code{makeDepmix} creates an object of class \code{depmix}.  This
+	function is meant for full control, e.g. specifying each response model
+	and the transition and prior models 'by hand'.  For the default easier
+	specification of models, please see \code{\link{depmix}}.  This
+	function is meant for specifying one's own response models.
+	
+}
+
+\usage{
+	
+	makeDepmix(response, transition, prior, ntimes = NULL, stationary = TRUE, 
+    ...) 	
+	
+}
+
+\arguments{
+	
+	\item{response}{A two-dimensional list of response models. See
+	'Details'.}
+	
+	\item{transition}{A list of transition models, each created by a call
+	to \code{\link{transInit}} on for possibilities of specifying such
+	models.  The lenght of this list should be the nubmer of states of the
+	model.}
+	
+	\item{prior}{The initial state probabilities model; created through a
+	call to \code{\link{transInit}}.}
+
+	\item{ntimes}{A vector specifying the lengths of individual, ie
+		independent, time series. If not specified, the responses are
+		assumed to form a single time series.}
+	
+	\item{stationary}{Logical indicating whether the transition models
+		include time-varying covariates; used internally to determine the
+		dimensions of certain arrays, notably \code{trDens}.}
+		
+	\item{...}{Not used currently.}
+		
+}
+
+\details{ 
+
+	The function \code{makeDepmix} creates an S4 object of class \code{depmix},
+	which needs to be fitted using \code{\link{fit}} to optimize the
+	parameters. This function is provided to have full control, eg by
+	specifying one's own response models with distributions that are not
+	provided. 
+	
+	The response model(s) should be created by call(s) to
+	\code{\link{response}} or one's own created response models that should
+	extend the response class and have the following methods: dens, predict
+	and optionally fit.  The fit function should have an argument w,
+	providing the weights.  If the fit function is not provided,
+	optimization should be done by using Rdonlp (use method="donlp" in
+	calling fit on the depmix model, this is currently not done
+	automatically).  The first index of response models runs over the
+	states of the model, and the seconde index over the responses to be
+	modeled.
+	
+}
+
+\value{
+	
+See the \code{\link{depmix}} help page for the return value, a
+\code{depmix} object.
+
+}
+
+\author{Ingmar Visser & Maarten Speekenbrink}
+
+\seealso{
+
+	\code{\link{fit}}, \code{\link{transInit}}, \code{\link{response}},
+	\code{\link{depmix-methods}} for accessor functions to \code{depmix}
+	objects.
+
+}
+
+\examples{
+
+# below example recreates the model from the depmix help page albeit in a
+# roundabout way
+
+data(speed)   
+
+rModels <- list(
+	list(
+		GLMresponse(formula=rt~1,data=speed,family=gaussian(),pstart=c(5.52,.202)),
+		GLMresponse(formula=corr~1,data=speed,family=multinomial(),pstart=c(0.5,0.5))
+	),
+	list(
+		GLMresponse(formula=rt~1,data=speed,family=gaussian(),pstart=c(6.39,.24)),
+		GLMresponse(formula=corr~1,data=speed,family=multinomial(),pstart=c(.1,.9))
+	)
+)
+
+trstart=c(0.9,0.1,0.1,0.9)
+
+transition <- list()
+transition[[1]] <- transInit(~1,nstates=2,data=data.frame(1),pstart=c(trstart[1:2]))
+transition[[2]] <- transInit(~1,nstates=2,data=data.frame(1),pstart=c(trstart[3:4]))
+
+instart=c(0,1)
+inMod <- transInit(~1,ns=2,ps=instart,data=data.frame(rep(1,3)))
+
+mod <- makeDepmix(response=rModels,transition=transition,prior=inMod,ntimes=attr(speed,"ntimes"))
+
+logLik(mod)
+
+fm <- fit(mod)
+
+fm 
+
+summary(fm)
+
+}
+
+\keyword{methods}
+
+


Property changes on: trunk/man/makeDepmix.Rd
___________________________________________________________________
Name: svn:executable
   + *