[Depmix-commits] r169 - in trunk: . man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Jun 17 14:24:16 CEST 2008
Author: ingmarvisser
Date: 2008-06-17 14:24:16 +0200 (Tue, 17 Jun 2008)
New Revision: 169
Added:
trunk/man/mix-class.Rd
trunk/man/mix.fitted-class.Rd
Modified:
trunk/NAMESPACE
trunk/man/AIC.Rd
trunk/man/depmix-class.Rd
trunk/man/depmix-internal.Rd
trunk/man/depmix-methods.Rd
trunk/man/depmix.fit.Rd
trunk/man/mix.Rd
trunk/man/posterior.Rd
Log:
Added mix-class.Rd and mix.fitted-class.Rd help files and fixed some codoc issues
Modified: trunk/NAMESPACE
===================================================================
--- trunk/NAMESPACE 2008-06-17 10:31:00 UTC (rev 168)
+++ trunk/NAMESPACE 2008-06-17 12:24:16 UTC (rev 169)
@@ -10,7 +10,6 @@
forwardbackward,
llratio,
multinomial,
- binomial,
em,
viterbi,
mlogit
Modified: trunk/man/AIC.Rd
===================================================================
--- trunk/man/AIC.Rd 2008-06-17 10:31:00 UTC (rev 168)
+++ trunk/man/AIC.Rd 2008-06-17 12:24:16 UTC (rev 169)
@@ -1,26 +1,35 @@
\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 depmix objects}
+\title{Compute AIC and BIC for (dep-)mix objects}
+
\description{
-Compute AIC and BIC for depmix objects.
+ Compute AIC and BIC for \code{depmix} and \code{mix} objects.
}
+
\usage{
-AIC(object, ..., k = 2)
-BIC(object, ...)
+ AIC(object, ..., k = 2)
+ BIC(object, ...)
}
-%- maybe also 'usage' for other objects documented here.
+
\arguments{
- \item{object}{A \code{depmix} model.}
+ \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 and BIC
+ The value of the AIC or BIC respectively.
}
+
\references{}
+
\author{Ingmar Visser}
+
\keyword{htest}
Modified: trunk/man/depmix-class.Rd
===================================================================
--- trunk/man/depmix-class.Rd 2008-06-17 10:31:00 UTC (rev 168)
+++ trunk/man/depmix-class.Rd 2008-06-17 12:24:16 UTC (rev 169)
@@ -10,6 +10,10 @@
\alias{ntimes}
\alias{ntimes,depmix-method}
+\alias{nstates}
+\alias{nstates,depmix-method}
+
+
\title{Class "depmix"}
\description{A \code{\link{depmix}} model.}
Modified: trunk/man/depmix-internal.Rd
===================================================================
--- trunk/man/depmix-internal.Rd 2008-06-17 10:31:00 UTC (rev 168)
+++ trunk/man/depmix-internal.Rd 2008-06-17 12:24:16 UTC (rev 169)
@@ -7,13 +7,14 @@
\alias{lystig}
\alias{makeDepmix}
+\alias{makeMix}
\alias{makePriorModel}
\alias{makeResponseModels}
\alias{makeTransModels}
\alias{mlogit}
\alias{multinomial}
-\alias{nstates}
+
\alias{pa2conr}
\alias{viterbi}
\alias{viterbi2}
Modified: trunk/man/depmix-methods.Rd
===================================================================
--- trunk/man/depmix-methods.Rd 2008-06-17 10:31:00 UTC (rev 168)
+++ trunk/man/depmix-methods.Rd 2008-06-17 12:24:16 UTC (rev 169)
@@ -6,47 +6,62 @@
\alias{logLik}
\alias{logLik,depmix-method}
+\alias{logLik,mix-method}
\alias{nobs}
\alias{nobs,depmix-method}
+\alias{nobs,mix-method}
\alias{npar}
\alias{npar,depmix-method}
+\alias{npar,mix-method}
\alias{freepars}
\alias{freepars,depmix-method}
+\alias{freepars,mix-method}
\alias{setpars}
\alias{setpars,depmix-method}
+\alias{setpars,mix-method}
\alias{getpars}
\alias{getpars,depmix-method}
+\alias{getpars,mix-method}
-\title{ Depmix methods. }
+\title{ 'depmix' and 'mix' methods. }
\description{
-Computes the log likelihood of a depmix object.
+Various methods for \code{depmix} and \code{mix} objects.
}
\usage{
\S4method{logLik}{depmix}(object,method="lystig")
+ \S4method{logLik}{mix}(object,method="lystig")
\S4method{nobs}{depmix}(object, ...)
+ \S4method{nobs}{mix}(object, ...)
+
\S4method{npar}{depmix}(object)
+ \S4method{npar}{mix}(object)
+
\S4method{freepars}{depmix}(object)
+ \S4method{freepars}{mix}(object)
\S4method{setpars}{depmix}(object,values, which="pars",...)
+ \S4method{setpars}{mix}(object,values, which="pars",...)
+
\S4method{getpars}{depmix}(object,which="pars",...)
-
+ \S4method{getpars}{mix}(object,which="pars",...)
}
\arguments{
- \item{object}{A \code{depmix} object.}
+ \item{object}{A \code{depmix} or \code{mix} object.}
- \item{values}{To be used in \code{setpars} to set new parameter values.}
+ \item{values}{To be used in \code{setpars} to set new parameter values; see
+ the example.}
\item{method}{The log likelihood can be computed by either the forward
backward algorithm from Rabiner, 1989, or by the method of Lystig and
@@ -80,7 +95,7 @@
\item{freepars}{returns the number of non-fixed parameters.}
- \item{setpars}{returns a depmix object with new parameter values.}
+ \item{setpars}{returns a \code{(dep-)mix} object with new parameter values.}
\item{getpars}{returns a vector with the current parameter values.}
Modified: trunk/man/depmix.fit.Rd
===================================================================
--- trunk/man/depmix.fit.Rd 2008-06-17 10:31:00 UTC (rev 168)
+++ trunk/man/depmix.fit.Rd 2008-06-17 12:24:16 UTC (rev 169)
@@ -9,12 +9,19 @@
\alias{show,depmix.fitted-method}
\alias{summary,depmix.fitted-method}
-\title{Fit depmix models}
+\alias{mix.fit}
+\alias{fit,mix-method}
+\alias{show,mix.fitted-method}
+\alias{summary,mix.fitted-method}
+
+\title{Fit 'depmix' or 'mix' models}
+
\description{
- \code{fit} optimizes parameters of \code{\link{depmix}} models, optionally
- subject to general linear (in)equality constraints.}
+ \code{fit} optimizes parameters of \code{\link{depmix}} or
+ \code{\link{mix}} models, optionally subject to general linear
+ (in)equality constraints.}
\usage{
@@ -22,12 +29,18 @@
conrows.upper=0, conrows.lower=0, method=NULL,...)
\S4method{summary}{depmix.fitted}(object)
+
+ \S4method{fit}{mix}(object, fixed=NULL, equal=NULL, conrows=NULL,
+ conrows.upper=0, conrows.lower=0, method=NULL,...)
+ \S4method{summary}{mix.fitted}(object)
+
+
}
\arguments{
- \item{object}{An object of class \code{depmix}.}
+ \item{object}{An object of class \code{(dep-)mix}.}
\item{fixed}{Vector of mode logical indicating which parameters should
be fixed.}
Added: trunk/man/mix-class.Rd
===================================================================
--- trunk/man/mix-class.Rd (rev 0)
+++ trunk/man/mix-class.Rd 2008-06-17 12:24:16 UTC (rev 169)
@@ -0,0 +1,66 @@
+\name{mix-class}
+
+\docType{class}
+
+\alias{mix-class}
+
+\alias{nresp,mix-method}
+\alias{nstates,mix-method}
+\alias{ntimes,mix-method}
+
+\title{Class "mix"}
+\description{ A \code{\link{mix}} model. }
+
+\section{Objects from the Class}{
+Objects can be created by calls to \code{\link{mix}}.
+}
+
+\section{Slots}{
+
+ \describe{
+
+ \item{\code{response}:}{List of list of \code{response} objects.}
+
+ \item{\code{prior}:}{\code{\link{transInit}} object; model for the
+ prior probabilities, also unconditional probabilities}
+
+ \item{\code{dens}:}{Array of dimension sum(ntimes)*nresp*nstates
+ providing the densities of the observed responses for each state.}
+
+ \item{\code{init}:}{Array of dimension
+ \code{length(ntimes)}*nstates with the current predictions for the
+ initial state probabilities.}
+
+ \item{\code{nstates}:}{The number of states (classes) of the model.}
+
+ \item{\code{nresp}:}{The number of independent responses.}
+
+ \item{\code{ntimes}:}{A vector of 1's for each case; for internal
+ use.}
+
+ \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.}
+
+ }
+}
+
+\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{nresp}:}{The number of responses.}
+ \item{\code{nstates}:}{The number of states.}
+ \item{\code{ntimes}:}{The vector of independent time series lengths.}
+ }
+}
+
+\author{Ingmar Visser}
+
+\examples{
+ showClass("mix")
+}
+
+\keyword{classes}
Modified: trunk/man/mix.Rd
===================================================================
--- trunk/man/mix.Rd 2008-06-17 10:31:00 UTC (rev 168)
+++ trunk/man/mix.Rd 2008-06-17 12:24:16 UTC (rev 169)
@@ -68,7 +68,7 @@
The response model(s) are created by call(s) to \code{\link{response}}
providing the response formula and the family specifying the error
distribution. If response is a list of formulae, the \code{response}'s
- are assumed to be independent conditional on the latent state.
+ are assumed to be independent conditional on the latent class.
The prior density is modeled as a multinomial logistic. This model is
created by a call to \code{\link{transInit}}.
@@ -87,7 +87,7 @@
\value{
-\code{depmix} returns an object of class \code{depmix} which has the
+\code{mix} returns an object of class \code{mix} which has the
following slots:
\item{response}{A list of a list of response models; the first
@@ -100,9 +100,8 @@
\item{dens,init}{See \code{\link{mix-class}} help for details. For
internal use.}
- \item{ntimes}{A vector containing the lengths of independent time
- series; if data is provided, sum(ntimes) must be equal to
- nrow(data).}
+ \item{ntimes}{A vector made by \code{rep(1,nrow(data))}; for internal
+ use only.}
\item{nstates}{The number of states of the model.}
@@ -127,10 +126,6 @@
\references{
- On hidden Markov models: Lawrence R. Rabiner (1989). A tutorial on
- hidden Markov models and selected applications in speech recognition.
- \emph{Proceedings of IEEE}, 77-2, p. 267-295.
-
On latent class models: A. L. McCutcheon (1987). \emph{Latent class
analysis}. Sage Publications.
Added: trunk/man/mix.fitted-class.Rd
===================================================================
--- trunk/man/mix.fitted-class.Rd (rev 0)
+++ trunk/man/mix.fitted-class.Rd 2008-06-17 12:24:16 UTC (rev 169)
@@ -0,0 +1,69 @@
+\name{mix.fitted-class}
+
+\docType{class}
+
+\alias{mix.fitted-class}
+
+\title{Class "mix.fitted"}
+
+\description{A fitted \code{\link{mix}} model.}
+
+\section{Slots}{
+
+ A \code{mix.fitted} object is a \code{mix} object with three
+ additional slots, here is the complete list:
+
+ \describe{
+
+ \item{\code{response}:}{List of list of \code{response} 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{init}:}{Array of dimension \code{length(ntimes)}*nstates with
+ the current predictions for the initial state probabilities.}
+
+ \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.}
+
+ \item{\code{posterior}:}{Posterior (Viterbi) state sequence (not
+ implemented currently).}
+ }
+}
+
+\section{Details}{
+
+ The print function shows some convergence information, and the summary
+ method shows the parameter estimates.
+
+}
+
+\section{Extends}{
+ Class \code{"\linkS4class{mix}"}, directly.
+}
+
+\author{Ingmar Visser}
+
+\examples{
+ showClass("mix.fitted")
+}
+
+\keyword{classes}
Modified: trunk/man/posterior.Rd
===================================================================
--- trunk/man/posterior.Rd 2008-06-17 10:31:00 UTC (rev 168)
+++ trunk/man/posterior.Rd 2008-06-17 12:24:16 UTC (rev 169)
@@ -3,22 +3,26 @@
\alias{posterior}
\alias{posterior,depmix.fitted-method}
+\alias{posterior,mix.fitted-method}
+
\title{ Posterior states/classes }
\description{
- Return the posterior states for a fitted depmix object. In the case
- of a latent class or mixture model these are the class probabilities.
+ Return the posterior states for a fitted \code{(dep-)mix} object. In
+ the case of a latent class or mixture model these are the class
+ probabilities.
}
\usage{
\S4method{posterior}{depmix.fitted}(object)
+ \S4method{posterior}{mix.fitted}(object)
}
\arguments{
- \item{object}{A depmix object.}
+ \item{object}{A (dep-)mix object.}
}
\value{
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