Author: ingmarvisser
Date: 2008-03-17 23:35:32 +0100 (Mon, 17 Mar 2008)
New Revision: 84
Added:
trunk/man/depmix-internal.Rd
trunk/man/depmix.fitted-class.Rd
trunk/man/response-classes.Rd
Modified:
trunk/DESCRIPTION
Log:
Added help files internal, fitted class and response classes
Modified: trunk/DESCRIPTION
===================================================================
--- trunk/DESCRIPTION 2008-03-17 15:39:29 UTC (rev 83)
+++ trunk/DESCRIPTION 2008-03-17 22:35:32 UTC (rev 84)
@@ -4,7 +4,7 @@
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 (>= 2.6.0), nnet
+Depends: R (>= 2.6.0), nnet, methods
Suggests: Rdonlp2
Description: Fit latent (hidden) Markov models on mixed categorical and continuous (timeseries)
data, otherwise known as dependent mixture models
Added: trunk/man/depmix-internal.Rd
===================================================================
--- trunk/man/depmix-internal.Rd (rev 0)
+++ trunk/man/depmix-internal.Rd 2008-03-17 22:35:32 UTC (rev 84)
@@ -0,0 +1,61 @@
+\name{depmix-internal}
+
+\alias{dens}
+\alias{em}
+\alias{fb}
+\alias{logDens}
+\alias{lystig}
+\alias{makePriorModel}
+\alias{makeResponseModels}
+\alias{makeTransModels}
+
+\alias{mlogit}
+\alias{multinomial}
+\alias{nobs}
+\alias{nresp}
+\alias{nstates}
+\alias{ntimes}
+\alias{pa2conr}
+\alias{viterbi}
+\alias{viterbi.fb}
+
+\alias{dens,GLMresponse-method}
+\alias{dens,BINOMresponse-method}
+\alias{dens,NORMresponse-method}
+\alias{dens,MULTINOMresponse-method}
+\alias{dens,transInit-method}
+
+\alias{fit,GLMresponse-method}
+\alias{fit,BINOMresponse-method}
+\alias{fit,NORMresponse-method}w
+\alias{fit,MULTINOMresponse-method}
+\alias{fit,MVNresponse-method}
+\alias{fit,transInit-method}
+
+\alias{logLik,GLMresponse-method}
+
+\alias{predict,GLMresponse-method}
+\alias{predict,BINOMresponse-method}
+\alias{predict,NORMresponse-method}
+\alias{predict,MULTINOMresponse-method}
+\alias{predict,transInit-method}
+
+\alias{getpars,GLMresponse-method}
+\alias{setpars,GLMresponse-method}
+
+\alias{getdf,response,response-method}
+\alias{npar,response,response-method}
+
+\title{Depmix internal functions}
+
+\description{
+ Internal depmix functions, methods and classes.
+}
+
+\details{
+ These are not to be called by the user.
+}
+
+\author{Ingmar Visser}
+
+\keyword{methods}
Property changes on: trunk/man/depmix-internal.Rd
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/man/depmix.fitted-class.Rd
===================================================================
--- trunk/man/depmix.fitted-class.Rd (rev 0)
+++ trunk/man/depmix.fitted-class.Rd 2008-03-17 22:35:32 UTC (rev 84)
@@ -0,0 +1,67 @@
+\name{depmix.fitted-class}
+
+\docType{class}
+
+\alias{depmix.fitted-class}
+
+\title{Class "depmix.fitted"}
+
+\description{Class \code{depmix.fitted}.}
+
+\section{Slots}{
+
+ A \code{depmix.fitted} object is a \code{depmix} object with two
+ additional slots:
+
+ \describe{
+
+ \item{\code{response}:}{List of list of \code{response} objects.}
+
+ \item{\code{transition}}{List of \code{transInit} objects.}
+
+ \item{\code{prior}:}{\code{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
+ the current predictions for the initial state probabilities.}
+
+ \item{\code{stationary}:}{Logical indicating whether the transitions are
+ time-dependent or not; for internal use.}
+
+ \item{\code{ntimes}:}{A vector containing the lengths of independent time
+ series; if data is provided, sum(ntimes) must be equal to
+ nrow(data).}
+
+ \item{\code{nstates}:}{The number of states of the model.}
+
+ \item{\code{nresp}:}{The number of independent responses.}
+
+ \item{\code{npars}:}{The total number of parameters of the model. This is not
+ the degrees of freedom, ie there are redundancies in the
+ parameters, in particular in the multinomial models for the
+ transitions and prior.}
+
+ \item{\code{message}:}{This provides some information on convergence,
+ either from the EM algorithm or from Rdonlp2.}
+
+ \item{\code{conMat}:}{The linear constraint matrix, which has zero rows
+ if there were no constraints.}
+ }
+}
+
+\section{Details}{
+
+ The print function shows some convergence information, and the summary
+ method shows the parameter estimates.
+
+}
+
+\author{Ingmar Visser}
+
+\keyword{classes}
Property changes on: trunk/man/depmix.fitted-class.Rd
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/man/response-classes.Rd
===================================================================
--- trunk/man/response-classes.Rd (rev 0)
+++ trunk/man/response-classes.Rd 2008-03-17 22:35:32 UTC (rev 84)
@@ -0,0 +1,51 @@
+\name{response-classes}
+
+\docType{class}
+
+\alias{GLMresponse-class}
+\alias{transInit-class}
+
+\title{Class "GLmresponse" and class "transInit"}
+
+\description{Specific instances of response models for depmix models.}
+
+\section{Slots}{
+
+ Both \code{GLMresponse} and \code{transInit} contain the
+ \code{response}-class. In addition to the slots of that class, these
+ classes have the following slots:
+
+ \describe{
+ \item{\code{formula}:}{A formula that specifies the model.}
+ \item{\code{family}:}{A family object specifying the link function etc.}
+ }
+
+}
+
+\details{
+
+ The \code{GLMresponse}-class offers an interface to the glm functions
+ that are subsequently used in fitting the \code{depmix} model of which
+ the response is a part.
+
+ The \code{transInit} is an extension of \code{response} that is used to
+ model the transition matrix and the initial state probabilities by the
+ use of a multinomial logistic model, the difference being that in fact
+ the response is missing as the transitions between states are not
+ observed. This class has its own fit function which is an interface to
+ the multinom function in nnet.
+
+}
+
+\section{Accessor Functions}{
+ The following functions should be used for accessing the corresponding
+ slots:
+ \describe{
+ \item{\code{npar}:}{The number of parameters of the model.}
+ \item{\code{getdf}:}{The number of non-fixed parameters.}
+ }
+}
+
+\author{Ingmar Visser}
+
+\keyword{classes}
Property changes on: trunk/man/response-classes.Rd
___________________________________________________________________
Name: svn:executable
+ *