[Depmix-commits] r141 - trunk/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Jun 9 16:22:52 CEST 2008
Author: ingmarvisser
Date: 2008-06-09 16:22:51 +0200 (Mon, 09 Jun 2008)
New Revision: 141
Added:
trunk/man/AIC.Rd
trunk/man/depmix-methods.Rd
trunk/man/depmixS4-package.Rd
trunk/man/posterior.Rd
Modified:
trunk/man/balance.Rd
trunk/man/depmix-internal.Rd
trunk/man/depmix.Rd
trunk/man/depmix.fit.Rd
trunk/man/response-classes.Rd
trunk/man/response.Rd
trunk/man/simulate.Rd
trunk/man/speed.Rd
Log:
Restructured help files somewhat
Added: trunk/man/AIC.Rd
===================================================================
--- trunk/man/AIC.Rd (rev 0)
+++ trunk/man/AIC.Rd 2008-06-09 14:22:51 UTC (rev 141)
@@ -0,0 +1,26 @@
+\name{AIC}
+\alias{AIC}
+\alias{AIC,depmix-method}
+\alias{BIC}
+\alias{BIC,depmix-method}
+
+\title{Compute AIC and BIC for depmix objects}
+\description{
+Compute AIC and BIC for depmix objects.
+}
+\usage{
+AIC(object, ..., k = 2)
+BIC(object, ...)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+ \item{object}{A \code{depmix} model.}
+ \item{\dots}{Not used currently.}
+ \item{k}{The penalty factor which defaults to 2.}
+}
+\value{
+ The value of the AIC and BIC
+}
+\references{}
+\author{Ingmar Visser}
+\keyword{htest}
Modified: trunk/man/balance.Rd
===================================================================
--- trunk/man/balance.Rd 2008-06-09 13:08:25 UTC (rev 140)
+++ trunk/man/balance.Rd 2008-06-09 14:22:51 UTC (rev 141)
@@ -19,8 +19,14 @@
\item{\code{sex}}{Participants' sex.}
\item{\code{agedays}}{Age in days.}
\item{\code{age}}{Age in years.}
- \item{\code{t1-t4}}{Trichotomously scored distance items.}
- \item{\code{d1-d4}}{Dichotomously scored distance items.}
+ \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.}
}
}
Modified: trunk/man/depmix-internal.Rd
===================================================================
--- trunk/man/depmix-internal.Rd 2008-06-09 13:08:25 UTC (rev 140)
+++ trunk/man/depmix-internal.Rd 2008-06-09 14:22:51 UTC (rev 141)
@@ -16,11 +16,17 @@
\alias{nstates}
\alias{pa2conr}
\alias{viterbi}
+\alias{viterbi2}
\alias{viterbi.fb}
\alias{dens,GLMresponse-method}
\alias{dens,BINOMresponse-method}
\alias{dens,NORMresponse-method}
+
+\alias{dens,GAMMAresponse-method}
+\alias{dens,POISSONresponse-method}
+\alias{dens,MVNresponse-method}
+
\alias{dens,MULTINOMresponse-method}
\alias{dens,transInit-method}
@@ -56,4 +62,4 @@
\author{Ingmar Visser}
-\keyword{methods}
+\keyword{internal}
Added: trunk/man/depmix-methods.Rd
===================================================================
--- trunk/man/depmix-methods.Rd (rev 0)
+++ trunk/man/depmix-methods.Rd 2008-06-09 14:22:51 UTC (rev 141)
@@ -0,0 +1,76 @@
+\name{depmix-methods}
+
+\docType{methods}
+
+\alias{logLik}
+\alias{logLik,depmix-method}
+
+\alias{nobs}
+\alias{nobs,depmix-method}
+
+\alias{npar}
+\alias{npar,depmix-method}
+
+\alias{freepars}
+\alias{freepars,depmix-method}
+
+\alias{setpars}
+\alias{setpars,depmix-method}
+
+\alias{getpars}
+\alias{getpars,depmix-method}
+
+\title{ The log likelihood. }
+\description{
+Computes the log likelihood of a depmix object.
+}
+\usage{
+ \S4method{logLik}{depmix}(object)
+
+ \S4method{nobs}{depmix}(object)
+
+ \S4method{npar}{depmix}(object)
+ \S4method{freepars}{depmix}(object)
+ \S4method{setpars}{depmix}(object,which="pars",...)
+ \S4method{getpars}{depmix}(object,which="pars",...)
+
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+ \item{object}{A \code{depmix} pobject}
+
+ \item{which}{The default "pars" returns a vector of all parameters of a
+ \code{depmix} object; the alternative value "fixed" return a
+ logical vector of the same length indicating which parameters are
+ fixed. The setpars functions sets parameters (or the logical fixed
+ vector) to new values; \code{setpars} also recomputes the dens,
+ trans and init slots of \code{depmix} objects. Note that the
+ \code{getpars} and \code{setpars} functions for \code{depmix}
+ objects simply call the functions of the same name for the response
+ and transition models.}
+
+ \item{...}{Not used currently.}
+
+}
+\value{
+
+ \item{logLik} {returns a \code{logLik} object with attributes \code{df} and \code{nobs}.}
+
+ \item{nobs} {returns the number of observations (used in computing the BIC).}
+
+ \item{npar} {returns the number of paramters of a model.}
+
+ \item{freepars} {returns the number of non-fixed parameters.}
+
+ \item{setpars} {returns a depmix object with new parameter values.}
+
+ \item{getpars} {returns a vector with the current parameter values.}
+
+}
+\author{Ingmar Visser}
+\examples{
+
+}
+
+\keyword{methods}
+
Modified: trunk/man/depmix.Rd
===================================================================
--- trunk/man/depmix.Rd 2008-06-09 13:08:25 UTC (rev 140)
+++ trunk/man/depmix.Rd 2008-06-09 14:22:51 UTC (rev 141)
@@ -3,31 +3,12 @@
\docType{methods}
-\alias{depmixS4}
\alias{depmix}
\alias{depmix,ANY-method}
-\alias{logLik}
-\alias{logLik,depmix-method}
+\alias{show}
+\alias{summary}
-\alias{BIC}
-\alias{BIC,depmix-method}
-
-\alias{nobs}
-\alias{nobs,depmix-method}
-
-\alias{npar}
-\alias{npar,depmix-method}
-
-\alias{freepars}
-\alias{freepars,depmix-method}
-
-\alias{setpars}
-\alias{setpars,depmix-method}
-
-\alias{getpars}
-\alias{getpars,depmix-method}
-
\alias{show,depmix-method}
\alias{summary,depmix-method}
@@ -54,15 +35,7 @@
ntimes=NULL,...)
\S4method{summary}{depmix}(object)
- \S4method{logLik}{depmix}(object)
-
- \S4method{BIC}{depmix}(object)
- \S4method{nobs}{depmix}(object)
- \S4method{npar}{depmix}(object)
- \S4method{freepars}{depmix}(object)
- \S4method{setpars}{depmix}(object,which="pars",...)
- \S4method{getpars}{depmix}(object,which="pars",...)
}
@@ -103,16 +76,6 @@
independent, time series. If not specified, the responses are
assumed to form a single time series. If the data argument has an
attribute ntimes, then this is used.}
-
- \item{which}{The default "pars" returns a vector of all parameters of a
- \code{depmix} object; the alternative value "fixed" return a
- logical vector of the same length indicating which parameters are
- fixed. The setpars functions sets parameters (or the logical fixed
- vector) to new values; \code{setpars} also recomputes the dens,
- trans and init slots of \code{depmix} objects. Note that the
- \code{getpars} and \code{setpars} functions for \code{depmix}
- objects simply call the functions of the same name for the response
- and transition models.}
\item{...}{Not used currently.}
@@ -178,12 +141,6 @@
parameters, in particular in the multinomial models for the
transitions and prior.}
-\code{logLik}, \code{AIC}, and \code{BIC} return the respective values
-associated with the current parameter values. \code{nobs} returns the
-number of observations, ie \code{sum(ntimes)} that is used in computing the
-\code{BIC}. \code{npar} returns the number of paramters of a model;
-\code{freepars} returns the number of non-fixed parameters.
-
}
\author{Ingmar Visser \email{i.visser at uva.nl}}
Modified: trunk/man/depmix.fit.Rd
===================================================================
--- trunk/man/depmix.fit.Rd 2008-06-09 13:08:25 UTC (rev 140)
+++ trunk/man/depmix.fit.Rd 2008-06-09 14:22:51 UTC (rev 141)
@@ -6,9 +6,6 @@
\alias{depmix.fit}
\alias{fit,depmix-method}
-\alias{posterior}
-\alias{posterior,depmix.fitted-method}
-
\alias{show,depmix.fitted-method}
\alias{summary,depmix.fitted-method}
@@ -24,7 +21,6 @@
\S4method{fit}{depmix}(object, fixed=NULL, equal=NULL, conrows=NULL,
conrows.upper=0, conrows.lower=0, method=NULL,...)
- \S4method{posterior}{depmix.fitted}(object,...)
\S4method{summary}{depmix.fitted}(object)
}
@@ -94,10 +90,6 @@
\item{message}{: Convergence information.}
\item{conMat}{: The constraint matrix A, see details.}
-
- \item{posterior}{: Returns a data.frame with nstates(object) + 1
- columns; the first column has the viterbi states, the other columns
- have the delta probabilities, see Rabiner (1989).}
The print method shows the \code{message} and the summary method
shows the parameter estimates.
Added: trunk/man/depmixS4-package.Rd
===================================================================
--- trunk/man/depmixS4-package.Rd (rev 0)
+++ trunk/man/depmixS4-package.Rd 2008-06-09 14:22:51 UTC (rev 141)
@@ -0,0 +1,53 @@
+\name{depmixS4-package}
+
+\alias{depmixS4-package}
+\alias{depmixS4}
+
+\docType{package}
+\title{
+depmixS4 provides classes for fitting hidden Markov models
+}
+\description{
+depmixS4 fits hidden Markov models on (multiple) sets of observations by the use
+of either EM or direct optimization of the log-likelihood; the latter is used to
+incorporate general linear constraints into models. The response densities for
+each state may be chosen from the GLM family, or a multinomial. User defined
+response densities are easy to add.
+}
+\details{
+\tabular{ll}{
+Package: \tab depmixS4\cr
+Type: \tab Package\cr
+Version: \tab 0.2\cr
+Date: \tab 2008-06-09\cr
+License: \tab GPL\cr
+}
+
+Model fitting is done in two steps; first, models are specified through the
+depmix function, which uses standard arguments to eg specify GLM densities
+for the responses; second, the model is fitted; the fit function is used to
+provide extra arguments concerning the optimization, such as providing
+constraints on parameters.
+
+}
+\author{
+Ingmar Visser & Maarten Speekenbrink
+Maintainer: i.visser at uva.nl
+}
+\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.
+
+}
+\keyword{ package }
+\seealso{
+\code{\link[<depmixS4>:<depmixS4>-package]{depmix}}
+}
+\examples{
+# These should be added at some point ...
+}
\ No newline at end of file
Added: trunk/man/posterior.Rd
===================================================================
--- trunk/man/posterior.Rd (rev 0)
+++ trunk/man/posterior.Rd 2008-06-09 14:22:51 UTC (rev 141)
@@ -0,0 +1,48 @@
+\name{posterior}
+
+\alias{posterior}
+
+\alias{posterior,depmix.fitted-method}
+
+\title{ Posterior states/classes }
+
+\description{
+
+ Compute the posterior states for a (fitted) depmix object. In the case
+ of a latent class or mixture model these are the class probabilities.
+
+}
+
+\usage{
+ \S4method{posterior}{depmix.fitted}(object,...)
+}
+
+\arguments{
+ \item{object}{A depmix object.}
+ \item{\dots}{Not currently used.}
+}
+
+\value{
+
+ \item{posterior}{: Returns a data.frame with nstates(object) + 1
+ columns; the first column has the viterbi states, the other columns
+ have the delta probabilities, see Rabiner (1989).}
+
+}
+
+\references{
+
+ 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.
+
+}
+
+\author{ Ingmar Visser }
+
+\examples{
+ # add some later
+}
+
+\keyword{ methods }
+
Modified: trunk/man/response-classes.Rd
===================================================================
--- trunk/man/response-classes.Rd 2008-06-09 13:08:25 UTC (rev 140)
+++ trunk/man/response-classes.Rd 2008-06-09 14:22:51 UTC (rev 141)
@@ -7,7 +7,7 @@
\alias{GLMresponse-class}
\alias{transInit-class}
-\title{Class "GLmresponse" and class "transInit"}
+\title{Class "GLMresponse" and class "transInit"}
\description{Specific instances of response models for \code{\link{depmix}}
models.}
@@ -55,4 +55,4 @@
\author{Ingmar Visser}
-\keyword{classes}
+\keyword{ methods }
Modified: trunk/man/response.Rd
===================================================================
--- trunk/man/response.Rd 2008-06-09 13:08:25 UTC (rev 140)
+++ trunk/man/response.Rd 2008-06-09 14:22:51 UTC (rev 141)
@@ -77,7 +77,7 @@
\code{getdf} returns the number of free parameters of a
\code{response} model.
-
+
}
\author{Ingmar Visser}
Modified: trunk/man/simulate.Rd
===================================================================
--- trunk/man/simulate.Rd 2008-06-09 13:08:25 UTC (rev 140)
+++ trunk/man/simulate.Rd 2008-06-09 14:22:51 UTC (rev 141)
@@ -1,7 +1,11 @@
-\name{simulate,depmix-method}
+\name{simulate}
\docType{method}
+\alias{simulate}
+
+\alias{simulate,response-method}
+\alias{simulate,depmix-method}
\alias{simulate,GLMresponse-method}
\alias{simulate,transInit-method}
@@ -9,46 +13,58 @@
\description{
-Random draws from \code{depmix} objects.
+ Random draws from \code{depmix} objects.
}
\usage{
- \S4method{simulate}{depmix}(object)
- \S4method{simulate}{response}(object)
+
+ \S4method{simulate}{depmix}(object, nsim=1, seed=NULL, times=NULL, ...)
+
+ \S4method{simulate}{response}(object)
+
\S4method{simulate}{GLMresponse}(object)
+
\S4method{simulate}{transInit}(object)
}
\arguments{
- \item{object}{Object to generate random draws. An object of class \code{depmix}, \code{response}, \code{transInit}}
- \item{nsim}{The number of draws.}
+
+ \item{object}{Object to generate random draws. An object of class
+ \code{depmix}, \code{response}, \code{transInit}}
+
+ \item{nsim}{The number of draws (one draw simulates a data set of the
+ size that is defined by ntimes); defaults to 1.}
+
\item{seed}{Set the seed.}
- \item{times}{An indicator vector indicating for which times in the complete
- series to generate the data. For internal use.}
+
+ \item{times}{An indicator vector indicating for which times in the
+ complete series to generate the data. For internal use.}
+
\item{...}{Not used currently.}
}
\details{
- For a \code{depmix} model, simulate generates \code{nsim} random state
- sequences, each of the same length as the observation sequence in the
- \code{depmix} model (i.e., \code{sum(ntimes(object))}. The state sequences
- are then used to generate \code{nsim} observation sequences of thee same
- length.
-
- Setting the \code{times} option selects the time points in the total
- state/observation sequence (i.e., counting is continued over ntimes).
- Usage of the \code{times} option is not recommended.
+ For a \code{depmix} model, simulate generates \code{nsim} random state
+ sequences, each of the same length as the observation sequence in the
+ \code{depmix} model (i.e., \code{sum(ntimes(object))}. The state
+ sequences are then used to generate \code{nsim} observation sequences
+ of thee same length.
+ Setting the \code{times} option selects the time points in the total
+ state/observation sequence (i.e., counting is continued over ntimes).
+ Usage of the \code{times} option is not recommended.
+
}
\value{
For a \code{depmix} object, a \code{list} with two elements;
- \code{states}, an N*nsim matrix with a state sequence in each column,
- and \code{responses}, an N*nobs*nsim array with observation sequences, where
- N = \code{sum(ntimes(object))}
+ \code{states}, an N*nsim matrix with a state sequence in each column,
+ and \code{responses}, an N*nobs*nsim array with observation sequences,
+ where N = \code{sum(ntimes(object))}
+
}
\author{Maarten Speekenbrink}
Modified: trunk/man/speed.Rd
===================================================================
--- trunk/man/speed.Rd 2008-06-09 13:08:25 UTC (rev 140)
+++ trunk/man/speed.Rd 2008-06-09 14:22:51 UTC (rev 141)
@@ -23,7 +23,14 @@
\usage{data(speed)}
-\format{Data.frame}
+\format{
+ A data frame with 439 observations on the following 3 variables.
+ \describe{
+ \item{\code{rt}}{a numeric vector}
+ \item{\code{corr}}{a numeric vector}
+ \item{\code{Pacc}}{a numeric vector}
+ }
+}
\source{
@@ -33,4 +40,9 @@
}
+\examples{
+data(speed)
+## maybe str(speed) ; plot(speed) ...
+}
+
\keyword{datasets}
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