[Depmix-commits] r331 - trunk/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Jan 29 15:14:48 CET 2010
Author: ingmarvisser
Date: 2010-01-29 15:14:48 +0100 (Fri, 29 Jan 2010)
New Revision: 331
Added:
trunk/man/GLMresponse.Rd
trunk/man/transInit.Rd
Removed:
trunk/man/response.Rd
Log:
GLMresponse and transInit now have their own help page.
Added: trunk/man/GLMresponse.Rd
===================================================================
--- trunk/man/GLMresponse.Rd (rev 0)
+++ trunk/man/GLMresponse.Rd 2010-01-29 14:14:48 UTC (rev 331)
@@ -0,0 +1,84 @@
+\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 uses functionality from the \code{nnet}
+ package to fit multinomial logistic models.
+
+ 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}
Property changes on: trunk/man/GLMresponse.Rd
___________________________________________________________________
Name: svn:executable
+ *
Name: svn:eol-style
+ native
Deleted: trunk/man/response.Rd
===================================================================
--- trunk/man/response.Rd 2010-01-29 14:13:30 UTC (rev 330)
+++ trunk/man/response.Rd 2010-01-29 14:14:48 UTC (rev 331)
@@ -1,86 +0,0 @@
-\name{response}
-
-\docType{method}
-
-\alias{response}
-\alias{transInit}
-\alias{GLMresponse}
-
-\alias{transInit,formula-method}
-\alias{GLMresponse,formula-method}
-
-\alias{getdf}
-\alias{getdf,response-method}
-
-\alias{show,GLMresponse-method}
-
-\title{Methods for creating depmix response models}
-
-\description{
-
-Create \code{response} objects for \code{\link{depmix}} models using
-formulae and family objects.
-
-}
-
-\usage{
-
- GLMresponse(formula, data=NULL, family=gaussian(), pstart=NULL,
- fixed=NULL, prob=TRUE, ...)
-
- transInit(formula, nstates, data=NULL, family=multinomial(),
- 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; see the \code{\link{responses}} help page
- a list of currently available options.}
- \item{pstart}{Starting values for the coefficients and other
- parameters, ie 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{nstates}{The number of states of the model.}
- \item{object}{Object of class response.}
- \item{...}{Not used currently.}
-}
-
-\details{
-
- Both methods use the familiar formula interface from \code{\link{glm}}
- to specify how responses (or transition or prior parameters) depend on
- covariates/predictors.
-
- The \code{GLMresponse} model is an interface to the \code{glm}
- functions of which the functionality is leant: predict, fit and
- density functions.
-
- The \code{transInit} response model provides functionality for
- multinomial responses that are currently fit using nnet (this may
- change in the future but this should not affect the interface of this
- function). Note that the transInit model actually lacks a reponse, ie
- the y-slot is empty, at the time of construction, as the transitions
- are not observed.
-
-}
-
-\value{
-
- \code{GLMresponse} and \code{transInit} return objects of class
- \code{GLMresponse} and \code{transInit} respectively; both classes
- extend the \code{\link{response-class}}.
-
- \code{getdf} returns the number of free parameters of a
- \code{response} model.
-
-}
-
-\author{Ingmar Visser & Maarten Speekenbrink}
-
-\keyword{methods}
Added: trunk/man/transInit.Rd
===================================================================
--- trunk/man/transInit.Rd (rev 0)
+++ trunk/man/transInit.Rd 2010-01-29 14:14:48 UTC (rev 331)
@@ -0,0 +1,77 @@
+\name{transInit}
+
+\docType{method}
+
+\alias{transInit}
+
+\alias{transInit,formula-method}
+
+\title{Methods for creating depmix transition and initial probability models}
+
+\description{
+
+Create \code{transInit} objects for \code{\link{depmix}} models using
+formulae and family objects.
+
+}
+
+\usage{
+
+ transInit(formula, nstates, data=NULL, family=multinomial(),
+ pstart=NULL, fixed=NULL, prob=TRUE, ...)
+}
+
+\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; see details.}
+ \item{pstart}{Starting values for the coefficients.}
+ \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{nstates}{The number of states of the model.}
+ \item{...}{Not used currently.}
+}
+
+\details{
+
+ The \code{transInit} model provides functionality for the multinomial
+ probabilities of the transitions between states, as well as for the
+ prior or initial probabilities. These probabilities may depend on
+ (time-varying) covariates. Currently, the only option for the family
+ object is the multinomial with a logistic link function. In
+ particular, the transition probabilities are modeled as baseline
+ logistic multinomials (see Agresti, 2002, p. 272 ff.).
+
+ Start values for the parameters may be provided using the \code{pstart}
+ argument; these can be provided as probabilities, the default option,
+ or as baseline logistic parameters, use the \code{prob} argument to
+ specify the chosen option. The default baseline category is set to 1,
+ which can be modified through calling, say, family=multinomial(base=2).
+
+ Note that the transInit model extends the \code{\link{response-class}},
+ but that it actually lacks a reponse, i.e. the y-slot is empty, at the
+ time of construction, as the transitions are not observed.
+
+}
+
+\value{
+
+ \code{transInit} return objects of class \code{transInit}; this class
+ extends the \code{\link{response-class}}.
+
+}
+
+\references{
+
+ Agresti, A. (2002). \emph{Categorical Data Analysis}. Wiley series in
+ probability and mathematical statistics. Wiley-Interscience, Hoboken,
+ NJ, 2 edition.
+
+}
+
+\author{Ingmar Visser & Maarten Speekenbrink}
+
+\keyword{methods}
Property changes on: trunk/man/transInit.Rd
___________________________________________________________________
Name: svn:executable
+ *
Name: svn:eol-style
+ native
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