[Depmix-commits] r456 - in pkg/depmixS4: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Mar 22 13:02:48 CET 2011
Author: ingmarvisser
Date: 2011-03-22 13:02:48 +0100 (Tue, 22 Mar 2011)
New Revision: 456
Removed:
pkg/depmixS4/R/depmixAIC.R
pkg/depmixS4/R/depmixBIC.R
pkg/depmixS4/man/AIC.Rd
Modified:
pkg/depmixS4/DESCRIPTION
pkg/depmixS4/NAMESPACE
pkg/depmixS4/R/allGenerics.R
pkg/depmixS4/man/depmixS4-package.Rd
Log:
Using AIC/BIC/logLik/nobs generics from stats/stats4 rather than defining them anew (which gave clashes with other packages that did the same).
Modified: pkg/depmixS4/DESCRIPTION
===================================================================
--- pkg/depmixS4/DESCRIPTION 2011-03-22 10:31:02 UTC (rev 455)
+++ pkg/depmixS4/DESCRIPTION 2011-03-22 12:02:48 UTC (rev 456)
@@ -1,10 +1,10 @@
Package: depmixS4
-Version: 1.0-2
-Date: 2011-02-15
+Version: 1.0-3
+Date: 2011-03-22
Title: Dependent Mixture Models - Hidden Markov Models of GLMs and Other Distributions in S4
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 (>= 2.11.1), stats, nnet, methods, MASS, Rsolnp
+Depends: R (>= 2.12.2), stats, nnet, methods, MASS, Rsolnp, stats4
Suggests: Rdonlp2, gamlss, gamlss.dist
Description: Fit latent (hidden) Markov models on mixed categorical and continuous (timeseries)
data, otherwise known as dependent mixture models
Modified: pkg/depmixS4/NAMESPACE
===================================================================
--- pkg/depmixS4/NAMESPACE 2011-03-22 10:31:02 UTC (rev 455)
+++ pkg/depmixS4/NAMESPACE 2011-03-22 12:02:48 UTC (rev 456)
@@ -1,6 +1,8 @@
import(methods)
-importFrom(stats, predict, simulate, AIC, logLik)
+importFrom(stats, predict, simulate)
+
+importFrom(stats4, AIC, BIC, logLik)
export(
makeDepmix,
@@ -14,7 +16,8 @@
em,
em.control,
viterbi,
- mlogit
+ mlogit,
+ logLik
)
exportClasses(
@@ -30,9 +33,7 @@
transInit
)
-exportMethods(
- AIC,
- BIC,
+exportMethods(
fit,
getConstraints,
npar,
@@ -51,10 +52,10 @@
transInit,
setpars,
getpars,
- logLik,
predict,
dens,
show,
- simulate,
- summary
+ simulate,
+ summary,
+ logLik
)
Modified: pkg/depmixS4/R/allGenerics.R
===================================================================
--- pkg/depmixS4/R/allGenerics.R 2011-03-22 10:31:02 UTC (rev 455)
+++ pkg/depmixS4/R/allGenerics.R 2011-03-22 12:02:48 UTC (rev 456)
@@ -9,6 +9,7 @@
require(MASS)
require(nnet)
require(Rsolnp)
+ require(stats4)
}
.Last.lib <- function(libpath) {}
@@ -26,10 +27,10 @@
setGeneric("transInit", function(formula, nstates, data = NULL, family = multinomial(),
pstart = NULL, fixed = NULL, prob=TRUE, ...) standardGeneric("transInit"))
+# extractors/set functions
+
setGeneric("npar", function(object, ...) standardGeneric("npar"))
-setGeneric("nobs", function(object, ...) standardGeneric("nobs"))
-
setGeneric("ntimes", function(object, ...) standardGeneric("ntimes"))
setGeneric("nstates", function(object, ...) standardGeneric("nstates"))
@@ -38,43 +39,42 @@
setGeneric("freepars", function(object, ...) standardGeneric("freepars"))
+setGeneric("getdf",function(object) standardGeneric("getdf"))
+
setGeneric("nlin", function(object, ...) standardGeneric("nlin"))
-# setGeneric("getModel", function(object, ...) standardGeneric("getModel"))
+setGeneric("nobs", function(object, ...) standardGeneric("nobs"))
-# setGeneric("logLik", function(object, ...) standardGeneric("logLik"))
-
-setGeneric("fit", function(object, ...) standardGeneric("fit"))
-
setGeneric("getConstraints", function(object, ...) standardGeneric("getConstraints"))
-setGeneric("posterior", function(object, ...) standardGeneric("posterior"))
+setGeneric("is.stationary", function(object,...) standardGeneric("is.stationary"))
-setGeneric("forwardbackward", function(object, ...) standardGeneric("forwardbackward"))
+setGeneric("setpars", function(object,values,which="pars",...) standardGeneric("setpars"))
-setGeneric("simulate", function(object,nsim=1,seed=NULL, ...) standardGeneric("simulate"))
+setGeneric("getpars", function(object,which="pars",...) standardGeneric("getpars"))
-setGeneric("predict", function(object, ...) standardGeneric("predict"))
-# setGeneric("AIC", function(object, ..., k=2) standardGeneric("AIC"))
+# functions
+setGeneric("fit", function(object, ...) standardGeneric("fit"))
-setGeneric("BIC", function(object, ...) standardGeneric("BIC"))
+setGeneric("posterior", function(object, ...) standardGeneric("posterior"))
-setGeneric("getdf",function(object) standardGeneric("getdf"))
+setGeneric("forwardbackward", function(object, ...) standardGeneric("forwardbackward"))
-setGeneric("setpars", function(object,values,which="pars",...) standardGeneric("setpars"))
+setGeneric("simulate", function(object,nsim=1,seed=NULL, ...) standardGeneric("simulate"))
-setGeneric("getpars", function(object,which="pars",...) standardGeneric("getpars"))
-
setGeneric("logDens",function(object,...) standardGeneric("logDens"))
setGeneric("dens",function(object,...) standardGeneric("dens"))
-setGeneric("summary")
+setGeneric("predict", function(object, ...) standardGeneric("predict"))
-setGeneric("ntimes", function(object, ...) standardGeneric("ntimes"))
-setGeneric("nresp", function(object, ...) standardGeneric("nresp"))
+# redundant??
-setGeneric("is.stationary", function(object,...) standardGeneric("is.stationary"))
+# setGeneric("getModel", function(object, ...) standardGeneric("getModel"))
+# these are imported from stats4
+# setGeneric("logLik", function(object, ...) standardGeneric("logLik"))
+# setGeneric("AIC", function(object, ..., k=2) standardGeneric("AIC"))
+# setGeneric("BIC", function(object, ...) standardGeneric("BIC"))
Deleted: pkg/depmixS4/R/depmixAIC.R
===================================================================
--- pkg/depmixS4/R/depmixAIC.R 2011-03-22 10:31:02 UTC (rev 455)
+++ pkg/depmixS4/R/depmixAIC.R 2011-03-22 12:02:48 UTC (rev 456)
@@ -1,13 +0,0 @@
-# depends on logLik and freepars
-setMethod("AIC", signature(object="depmix"),
- function(object, ..., k=2){
- c(-2 * logLik(object) + freepars(object) * k)
- }
-)
-
-# depends on logLik and freepars
-setMethod("AIC", signature(object="mix"),
- function(object, ..., k=2){
- c(-2 * logLik(object) + freepars(object) * k)
- }
-)
\ No newline at end of file
Deleted: pkg/depmixS4/R/depmixBIC.R
===================================================================
--- pkg/depmixS4/R/depmixBIC.R 2011-03-22 10:31:02 UTC (rev 455)
+++ pkg/depmixS4/R/depmixBIC.R 2011-03-22 12:02:48 UTC (rev 456)
@@ -1,12 +0,0 @@
-# depends on logLik, freepars and nobs
-setMethod("BIC", signature(object="depmix"),
- function(object, ...){
- c(-2 * logLik(object) + freepars(object) * log(nobs(object)))
- }
-)
-
-setMethod("BIC", signature(object="mix"),
- function(object, ...){
- c(-2 * logLik(object) + freepars(object) * log(nobs(object)))
- }
-)
Deleted: pkg/depmixS4/man/AIC.Rd
===================================================================
--- pkg/depmixS4/man/AIC.Rd 2011-03-22 10:31:02 UTC (rev 455)
+++ pkg/depmixS4/man/AIC.Rd 2011-03-22 12:02:48 UTC (rev 456)
@@ -1,48 +0,0 @@
-\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 (dep-)mix objects}
-
-\description{
- Compute AIC and BIC for \code{depmix} and \code{mix} objects.
-}
-
-\usage{
- AIC(object, ..., k = 2)
- BIC(object, ...)
-}
-
-\arguments{
- \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 or BIC respectively.
-}
-
-\details{
- The \code{n} that is used in the BIC is \code{sum(ntimes(object))}, where
- object is the model under consideration.
-}
-
-\references{
- H. Akaike. Information theory and an extension of the maximum likelihood
- principle. In B. N. Petrov and F. Csaki, editors, Second International
- Symposium on Information Theory, p. 267-281. Budapest: Academiai Kiado, 1973.
-
- G. Schwarz. Estimating the dimension of a model. Annals of Statistics,
- volume 6, p. 4761-464, 1978.
-}
-
-\author{Ingmar Visser}
-
-\keyword{htest}
Modified: pkg/depmixS4/man/depmixS4-package.Rd
===================================================================
--- pkg/depmixS4/man/depmixS4-package.Rd 2011-03-22 10:31:02 UTC (rev 455)
+++ pkg/depmixS4/man/depmixS4-package.Rd 2011-03-22 12:02:48 UTC (rev 456)
@@ -34,8 +34,8 @@
\tabular{ll}{
Package: \tab depmixS4\cr
Type: \tab Package\cr
- Version: \tab 1.0-0\cr
- Date: \tab 2010-08-04\cr
+ Version: \tab 1.0-3\cr
+ Date: \tab 2011-03-22\cr
License: \tab GPL\cr
}
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