[Depmix-commits] r72 - in trunk: R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Mar 7 15:52:11 CET 2008
Author: ingmarvisser
Date: 2008-03-07 15:52:10 +0100 (Fri, 07 Mar 2008)
New Revision: 72
Modified:
trunk/R/allGenerics.R
trunk/man/depmix-class.Rd
trunk/man/depmix.fit.Rd
trunk/man/response-class.Rd
Log:
Updated help files and removed some errors in them the package now builds
Modified: trunk/R/allGenerics.R
===================================================================
--- trunk/R/allGenerics.R 2008-03-07 14:40:09 UTC (rev 71)
+++ trunk/R/allGenerics.R 2008-03-07 14:52:10 UTC (rev 72)
@@ -7,6 +7,8 @@
setGeneric("depmix", function(response=any, transition=any, ...) standardGeneric("depmix"))
+setGeneric("npar", function(object, ...) standardGeneric("npar"))
+
setGeneric("nobs", function(object, ...) standardGeneric("nobs"))
setGeneric("ntimes", function(object, ...) standardGeneric("ntimes"))
Modified: trunk/man/depmix-class.Rd
===================================================================
--- trunk/man/depmix-class.Rd 2008-03-07 14:40:09 UTC (rev 71)
+++ trunk/man/depmix-class.Rd 2008-03-07 14:52:10 UTC (rev 72)
@@ -6,46 +6,46 @@
\title{Class "depmix"}
\description{A \code{\link{depmix}} model.}
\usage{
-\S4method{fit}{depmix}(object)
-\S4method{posterior}{depmix}(object)
+ \S4method{fit}{depmix}(object)
+ \S4method{posterior}{depmix}(object)
}
\arguments{
- \item{object}{An object of class "depmix".}
+ \item{object}{An object of class "depmix".}
}
\section{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.}
- }
+ \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.}
+ }
}
\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.}
- }
+ 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}
\keyword{classes}
Modified: trunk/man/depmix.fit.Rd
===================================================================
--- trunk/man/depmix.fit.Rd 2008-03-07 14:40:09 UTC (rev 71)
+++ trunk/man/depmix.fit.Rd 2008-03-07 14:52:10 UTC (rev 72)
@@ -1,7 +1,5 @@
\name{fit}
-
\docType{method}
-
\alias{fit}
\alias{depmix.fit}
\alias{fit,depmix-method}
@@ -12,10 +10,10 @@
\title{Method fit}
\description{\code{fit} optimizes parameters of depmix models, possibly
-subject to general linear (in)equality constraints.}
+ subject to general linear (in)equality constraints.}
\usage{
-
+
\S4method{fit}{depmix}(object, w=NULL, fixed=NULL, equal=NULL, conrows=NULL,
conrows.upper=0, conrows.lower=0, method=c("em","donlp"),...)
@@ -41,7 +39,7 @@
linear constraints on the parameters and if the transition model has
no covariates. Otherwise the general optimizer donlp is used which
handles general linear (in-)equality constraints.
-
+
Three types of constraints can be specified on the parameters: fixed,
equality, and general constraints. Constraint vectors should be of
length npar(object). See help on getpars and setpars about the
@@ -72,15 +70,14 @@
}
\value{
- \code{fit} returns an object of class depmix.fitted which contains
+ \code{fit} returns an object of class \code{depmix.fitted} which contains
the original depmix object, and further has slots:
- \describe{
- \item{message:}{Convergence information.}
- \item{conMat:}{The constraint matrix A, see details.}
- \item{posterior:}{The posterior state probabilities.}
- }
+ message: Convergence information.
+ conMat: The constraint matrix A, see details.
+ posterior: The posterior state probabilities.
+
The print function shows the \code{message} and the parameter
estimates.
Modified: trunk/man/response-class.Rd
===================================================================
--- trunk/man/response-class.Rd 2008-03-07 14:40:09 UTC (rev 71)
+++ trunk/man/response-class.Rd 2008-03-07 14:52:10 UTC (rev 72)
@@ -1,8 +1,6 @@
\name{response-class}
\docType{class}
\alias{response-class}
-\alias{posterior}
-\alias{posterior,response-method}
\title{Class "response"}
\description{A \code{\link{response}} model for depmix models.}
\arguments{
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