[Depmix-commits] r342 - in trunk: . inst man

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Thu Feb 11 16:49:13 CET 2010


Author: ingmarvisser
Date: 2010-02-11 16:49:13 +0100 (Thu, 11 Feb 2010)
New Revision: 342

Removed:
   trunk/COPYING
   trunk/DESCRIPTION
   trunk/NAMESPACE
   trunk/NEWS
   trunk/R/
   trunk/README
   trunk/data/
   trunk/inst/CITATION
   trunk/inst/doc/
   trunk/man/AIC.Rd
   trunk/man/GLMresponse.Rd
   trunk/man/balance.Rd
   trunk/man/depmix-class.Rd
   trunk/man/depmix-internal.Rd
   trunk/man/depmix-methods.Rd
   trunk/man/depmix.Rd
   trunk/man/depmix.fit.Rd
   trunk/man/depmix.fitted-class.Rd
   trunk/man/depmix.sim-class.Rd
   trunk/man/depmixS4-package.Rd
   trunk/man/forwardbackward.Rd
   trunk/man/llratio.Rd
   trunk/man/makeDepmix.Rd
   trunk/man/mix-class.Rd
   trunk/man/mix.Rd
   trunk/man/mix.fitted-class.Rd
   trunk/man/mix.sim-class.Rd
   trunk/man/posterior.Rd
   trunk/man/response-class.Rd
   trunk/man/response-classes.Rd
   trunk/man/responses.Rd
   trunk/man/simulate.Rd
   trunk/man/speed.Rd
   trunk/man/transInit.Rd
   trunk/tests/
Log:
emptied trunk directory

Deleted: trunk/COPYING
===================================================================
--- trunk/COPYING	2010-02-05 10:28:17 UTC (rev 341)
+++ trunk/COPYING	2010-02-11 15:49:13 UTC (rev 342)
@@ -1,340 +0,0 @@
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Deleted: trunk/DESCRIPTION
===================================================================
--- trunk/DESCRIPTION	2010-02-05 10:28:17 UTC (rev 341)
+++ trunk/DESCRIPTION	2010-02-11 15:49:13 UTC (rev 342)
@@ -1,12 +0,0 @@
-Package: depmixS4
-Version: 0.3-0
-Date: 2010-01-19
-Title: Dependent Mixture Models
-Author: Ingmar Visser <i.visser at uva.nl>, Maarten Speekenbrink <m.speekenbrink at ucl.ac.uk>
-Maintainer: Ingmar Visser <i.visser at uva.nl>
-Depends: R (>= 2.9.1), stats, nnet, methods, MASS, MCMCpack
-Suggests: Rdonlp2
-Description: Fit latent (hidden) Markov models on mixed categorical and continuous (timeseries)
-   data, otherwise known as dependent mixture models
-License: GPL (>=2)
-URL: http://depmix.r-forge.r-project.org/

Deleted: trunk/NAMESPACE
===================================================================
--- trunk/NAMESPACE	2010-02-05 10:28:17 UTC (rev 341)
+++ trunk/NAMESPACE	2010-02-11 15:49:13 UTC (rev 342)
@@ -1,58 +0,0 @@
-import(methods)
-
-importFrom(stats, predict, simulate, AIC, logLik)
-
-export(	
-	makeDepmix,
-	makeMix,
-	lystig,
-	fb,
-	forwardbackward,
-	MVNresponse,
-	llratio,
-	multinomial,
-	em,
-	viterbi,
-	mlogit
-)
-
-exportClasses(
-	depmix,
-	depmix.sim,
-	mix,
-	mix.sim,
-	depmix.fitted,
-	mix.fitted,
-	response,
-	GLMresponse,
-	MVNresponse,
-	transInit
-)
-
-exportMethods(
-	AIC,
-	BIC,
-	fit,
-	npar,
-	freepars,
-	nlin,
-	getdf,
-	nobs,
-	nresp,
-	ntimes,
-	nstates,
-	depmix,
-	mix,
-	posterior,
-	GLMresponse,
-	MVNresponse,
-	transInit,
-	setpars,
-	getpars,
-	logLik,
-	predict,
-	dens,
-	show,
-	simulate,
-	summary
-)

Deleted: trunk/NEWS
===================================================================
--- trunk/NEWS	2010-02-05 10:28:17 UTC (rev 341)
+++ trunk/NEWS	2010-02-11 15:49:13 UTC (rev 342)
@@ -1,81 +0,0 @@
-
-Changes in depmixS4 version 0.3-0
-  
-  o added multinomial response function with identity link (no covariates
-    allowed in such a model); useful when (many) boundary values occur; 
-    currently no constraints are used for such models, and hence only EM
-    can be used for optimization, or alternatively, if and when Rdonlp2
-    is used, sum constraints need to be added when fitting the model.
-    See ?GLMresponse for details. 
-
-  o added an example of how to specify a model with multivariate normal
-    responses (and fixed a bug in MVNresponse that prevented such models
-    from being specified in the first place). See ?makeDepmix for an 
-    example. 
-
-Changes in depmixS4 version 0.2-2
-
-  o fixed a warning produced when specifying conrows.upper and .lower in the
-    the fit function
-
-  o added error message in case the initial log likelihood is infeasible
-
-  o fixed a bug in the fit function for multinomial response models with 
-    covariates (thanks to Gilles Dutilh for spotting this)
-
-Changes in depmixS4 version 0.2-1
-
-  o fixed a bug in the Viterbi algorithm used to compute posterior states
-    (this bug was introduced in version 0.2-0)
-  
-  o restructured test files somewhat
-
-  o fixed a bug in the use of the conrows argument in the fit function (a 
-    missing drop=FALSE statement)
-
-  o updated help files for mix classes
-
-  o fixed a bug in setting the starting values of regression coefficients in 
-    prior and transInit models with covariates (thanks to Verena Schmittmann 
-    for reporting this)
-
-  o added newx argument to predict function of transInit objects, to be used
-    for predicting probabilities depending on covariates (useful in eg plotting
-    transition probabilities as function of a covariate)
-
-  o added example of the use of conrows argument in fitting functions and other 
-    minor updates in documentation
-  
-Changes in depmixS4 version 0.2-0
-
-  o restructured R and Rd (help) files; added depmixS4 help with a short
-    overview of the package and links to appropriate help files
-  
-  o added function 'simulate' to generate new data from a (fitted) model
-  
-  o added function 'forwardbackward' to access the forward and backward 
-    variables as well as the smoothed transition and state variables
-  
-  o added new glm distributions: gamma, poisson
-  
-  o added multivariate normal distribution
-  
-  o freepars now works correctly on both depmix and depmix.fitted objects
-  
-  o added function 'nlin' to compute the number of linear constraints in 
-    a fitted model object
-
-  o added mix class for mixture and latent class models; the depmix class 
-    extends this mix class and adds a transition model to it
-  
-  o added help file for makeDepmix to provide full control in specifying 
-    models
-  
-  o minor changes to make depmixS4 compatible with R 2.7.1
-  
-
-Changes in depmixS4 version 0.1-1
-
-  o adjusted for R 2.7.0
-
-First version released on CRAN: 0.1-0

Deleted: trunk/README
===================================================================
--- trunk/README	2010-02-05 10:28:17 UTC (rev 341)
+++ trunk/README	2010-02-11 15:49:13 UTC (rev 342)
@@ -1,17 +0,0 @@
-
-depmixS4 provides a framework for specifying and fitting hidden Markov models. Currently, it interfaces the glm functions to specify the state dependent measurement models. There is also a multinomial() family function that provides functionality for multinomial logistic responses with covariates. The transition matrix and the initial state probabilities are also modeled as multinomial logistics with the possibility of including covariates. Optimization is by default done by the EM algorithm. When linear constraints are included, Rdonlp2 is used for optimization (see details below). New response distributions can be added by extending the response-class and writing appropriate methods for it (dens, and getpars and setpars). depmixS4 also fits latent class and mixture models. 
-
-The latest development version of depmix can be found at: 
-https://r-forge.r-project.org/projects/depmix/
-
-
-DIFFERENCES BETWEEN DEPMIXS4 AND DEPMIX
-
-depmixS4 is a completely new implementation of the depmix package using S4 classes. Model specification now uses formulae and family objects, familiar from the lm and glm functions. Moreover, the transition matrix and the initial state probabilities (as well as multinomial responses) are now modeled by default as multinomial logistics with a baseline. Specification of linear constraints uses the same mechanism as was used in depmix, with the only difference that constraints are passed as arguments to the fit function rather than the model specification function. See the help files for further details.
-
-
-USING RDONLP2
-
-Optimization of models with (general) linear (in-)equality constraints can be done using the Rdonlp2 package, written Ryuichi Tamura(ry.tamura @ gmail.com), which is available from: http://arumat.net/Rdonlp2/
-
-Optimization with Rdonlp2 is automatically selected when constraints are specified in the fit function. 

Deleted: trunk/inst/CITATION
===================================================================
--- trunk/inst/CITATION	2010-02-05 10:28:17 UTC (rev 341)
+++ trunk/inst/CITATION	2010-02-11 15:49:13 UTC (rev 342)
@@ -1,15 +0,0 @@
-citHeader("To cite package depmix in publications, use the following:")
-
-citEntry(entry="Article",
-	title = "{depmixS4}: An R-package for fitting mixture models on mixed
-	multivariate data with Markov dependencies",
-	author = personList(person(first="Ingmar", last="Visser"), 
-		person(first="Maarten", last="Speekenbrink")),
-	journal = "R-package manual",
-	year = "2009",
-	url = "http://cran.r-project.org",
-	textVersion = paste("Ingmar Visser & Maarten Speekenbrink (2009).  DepmixS4: 
-	An R-package for fitting mixture models on mixed multivariate data with Markov
-	dependencies. R-package manual and introduction into Dependent 
-	Mixture models") 
-)

Deleted: trunk/man/AIC.Rd
===================================================================
--- trunk/man/AIC.Rd	2010-02-05 10:28:17 UTC (rev 341)
+++ trunk/man/AIC.Rd	2010-02-11 15:49:13 UTC (rev 342)
@@ -1,48 +0,0 @@
-\name{AIC}
-
-\alias{AIC}
-\alias{AIC,depmix-method}
-\alias{AIC,mix-method}
-
-\alias{BIC}
-\alias{BIC,depmix-method}
-\alias{BIC,mix-method}
-
-\title{Compute AIC and BIC for (dep-)mix objects}
-
-\description{
-	Compute AIC and BIC for \code{depmix} and \code{mix} objects.
-}
-
-\usage{
-	AIC(object, ..., k = 2)
-	BIC(object, ...)
-}
-
-\arguments{
-  \item{object}{A \code{depmix} or \code{mix} model.}
-  \item{\dots}{Not used currently.}
-  \item{k}{The penalty factor which defaults to 2.}
-}
-
-\value{
-	The value of the AIC or BIC respectively.
-}
-
-\details{
-	The \code{n} that is used in the BIC is \code{sum(ntimes(object))}, where
-	object is the model under consideration. 
-}
-
-\references{
-	H. Akaike. Information theory and an extension of the maximum likelihood 
-	principle. In B. N. Petrov and F. Csaki, editors, Second International
-	Symposium on Information Theory, p. 267-281. Budapest: Academiai Kiado, 1973.
-
-	G. Schwarz. Estimating the dimension of a model. Annals of Statistics, 
-	volume 6, p. 4761-464, 1978. 
-}
-
-\author{Ingmar Visser}
-
-\keyword{htest}

Deleted: trunk/man/GLMresponse.Rd
===================================================================
--- trunk/man/GLMresponse.Rd	2010-02-05 10:28:17 UTC (rev 341)
+++ trunk/man/GLMresponse.Rd	2010-02-11 15:49:13 UTC (rev 342)
@@ -1,90 +0,0 @@
-\name{GLMresponse}
-
-\docType{method}
-
-\alias{GLMresponse}
-\alias{GLMresponse,formula-method}
-
-\alias{getdf}
-\alias{getdf,response-method}
-
-\alias{show,GLMresponse-method}
-
-\title{Methods for creating depmix response models}
-
-\description{
-
-	Create \code{GLMresponse} objects for \code{\link{depmix}} models using
-	formulae and family objects.
-
-}
-
-\usage{
-	
-	GLMresponse(formula, data=NULL, family=gaussian(), pstart=NULL, 
-		fixed=NULL, prob=TRUE, ...)
-	
-	\S4method{getdf}{response}(object)
-}
-
-\arguments{
-	\item{formula}{A model \code{\link{formula}}.}
-	\item{data}{An optional data.frame to interpret the variables from the 
-		formula argument in.}	
-	\item{family}{A family object; }
-	\item{pstart}{Starting values for the coefficients and other
-		parameters, e.g. the standard deviation for the gaussian() family.}
-	\item{fixed}{Logical vector indicating which paramters are to be fixed.}
-	\item{prob}{Logical indicating whether the starting values for
-		multinomial() family models are probabilities or logistic
-		parameters (see details).}
-	\item{object}{Object of class response.}
-	\item{...}{Not used currently.}
-}
-
-\details{
-	
-	\code{GLMresponse} is the default driver for specifying response
-	distributions of \code{depmix} models.  It uses the familiar formula
-	interface from \code{\link{glm}} to specify how responses depend on
-	covariates/predictors.
-
-	Currently available options for the family argument are
-	\code{binomial}, \code{gaussian}, \code{poisson}, \code{Gamma}, and
-	\code{multinomial}.  Except for the latter option, the
-	\code{GLMresponse} model is an interface to the \code{glm} functions of
-	which the functionality is used: predict, fit and density functions.
-	
-	The \code{multinomial} model takes as link functions \code{mlogit}, the
-	default, and then uses functionality from the \code{nnet} package to
-	fit multinomial logistic models; it also takes \code{identity} as a
-	link function.  The latter is typically faster and is hence preferred
-	when no covariates are present.  Note that the sum constraint inherent
-	in such a model is automatically respected in the EM algorithm, but
-	must be supplied by the user in case of using Rdonlp optimization.
-	
-	See the \code{\link{responses}} help page for examples. 
-	
-}
-
-\value{
-	
-	\code{GLMresponse} returns an object of class \code{GLMresponse} which
-	extends the \code{\link{response-class}}.
-	
-	\code{getdf} returns the number of free parameters of a
-	\code{response} model.
-	
-}
-
-\seealso{
-	
-	\code{\link{makeDepmix}} has an example of specifying a model with a 
-	multivariate normal response and an example of how to add a user-defined
-	response model, in particular an ex-gauss distribution used for the
-	\code{speed} data. 
-}
-
-\author{Ingmar Visser & Maarten Speekenbrink}
-
-\keyword{methods}

Deleted: trunk/man/balance.Rd
===================================================================
--- trunk/man/balance.Rd	2010-02-05 10:28:17 UTC (rev 341)
+++ trunk/man/balance.Rd	2010-02-11 15:49:13 UTC (rev 342)
@@ -1,49 +0,0 @@
-\name{balance}
-
-\docType{data}
-
-\alias{balance}
-
-\title{Balance Scale Data}
-
-\description{Balance scale data of four distance items from 779 participants;
-participants ages are included.}
-
-\usage{data(balance)}
-
-\format{
-  
-	A data frame with 779 observations on the following variables. The full 
-	dataset is described and analyzed extensively in 
-	Jansen & Van der Maas (2002). The trichotomous data are left, balance, right. 
-	The dichotomous version of the data is scored correct, incorrect. 
-  
-  	\describe{
-		\item{\code{sex}}{Participants sex.}
-		\item{\code{agedays}}{Age in days.}
-		\item{\code{age}}{Age in years.}
-		\item{\code{t1}}{Trichotomously scored distance item.}
-		\item{\code{t2}}{Trichotomously scored distance item.}
-		\item{\code{t3}}{Trichotomously scored distance item.}
-		\item{\code{t4}}{Trichotomously scored distance item.}
-		\item{\code{d1}}{Dichotomously scored distance item.}
-		\item{\code{d2}}{Dichotomously scored distance item.}
-		\item{\code{d3}}{Dichotomously scored distance item.}
-		\item{\code{d4}}{Dichotomously scored distance item.}
-	}
-	
-}
-
-\source{
-
-	Brenda Jansen & Han van der Maas (2002). The development of
-	children's rule use on the balance scale task. \emph{Journal 
-	of experimental Child Psychology, 81}, p. 383-416.
-
-}
-
-\examples{
-data(balance)
-}
-
-\keyword{datasets}

Deleted: trunk/man/depmix-class.Rd
===================================================================
--- trunk/man/depmix-class.Rd	2010-02-05 10:28:17 UTC (rev 341)
+++ trunk/man/depmix-class.Rd	2010-02-11 15:49:13 UTC (rev 342)
@@ -1,73 +0,0 @@
-\name{depmix-class}
-
-\docType{class}
-
-\alias{depmix-class}
-
-\alias{nresp}
-\alias{nresp,depmix-method}
-
-\alias{ntimes}
-\alias{ntimes,depmix-method}
-
-\alias{nstates}
-\alias{nstates,depmix-method}
-
-
-\title{Class "depmix"}
-
-\description{A \code{\link{depmix}} model.}
-
-\section{Slots}{
-
-	\describe{
-
-	\item{\code{response}:}{List of list of \code{response} objects.}
-
-	\item{\code{transition}}{List of \code{\link{transInit}} objects.}
-	
-	\item{\code{prior}:}{\code{\link{transInit}} object.}
-	
-	\item{\code{dens}:}{Array of dimension sum(ntimes)*nresp*nstates
-		providing the densities of the observed responses for each state.}
-	
-	\item{\code{trDens}:}{Array of dimension \code{sum(ntimes)}*nstates
-		providing the probability of a state transition depending on the
-		predictors.}
-	
-	\item{\code{init}:}{Array of dimension \code{length(ntimes)}*nstates with 
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/depmix -r 342


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