[Pomp-commits] r456 - in pkg: R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed May 4 23:33:27 CEST 2011
Author: kingaa
Date: 2011-05-04 23:33:27 +0200 (Wed, 04 May 2011)
New Revision: 456
Added:
pkg/R/pfilter-methods.R
pkg/man/pfilter-methods.Rd
Modified:
pkg/R/aaa.R
pkg/R/mif-methods.R
pkg/R/pfilter.R
pkg/man/mif-methods.Rd
pkg/man/pfilter.Rd
Log:
- 'pred.mean', 'pred.var', and 'filter.mean' methods are now defined for 'pfilterd.pomp' objects (and not just 'mif' objects)
Modified: pkg/R/aaa.R
===================================================================
--- pkg/R/aaa.R 2011-05-04 21:32:39 UTC (rev 455)
+++ pkg/R/aaa.R 2011-05-04 21:33:27 UTC (rev 456)
@@ -15,3 +15,6 @@
setGeneric("logLik",function(object,...)standardGeneric("logLik"))
setGeneric("window",function(x,...)standardGeneric("window"))
setGeneric("continue",function(object,...)standardGeneric("continue"))
+setGeneric("pred.mean",function(object,...)standardGeneric("pred.mean"))
+setGeneric("pred.var",function(object,...)standardGeneric("pred.var"))
+setGeneric("filter.mean",function(object,...)standardGeneric("filter.mean"))
Modified: pkg/R/mif-methods.R
===================================================================
--- pkg/R/mif-methods.R 2011-05-04 21:32:39 UTC (rev 455)
+++ pkg/R/mif-methods.R 2011-05-04 21:33:27 UTC (rev 456)
@@ -1,17 +1,5 @@
## this file contains short definitions of methods for the 'mif' class
-pred.mean <- function (object, ...)
- stop("function ",sQuote("pred.mean")," is undefined for objects of class ",sQuote(class(object)))
-setGeneric('pred.mean')
-
-pred.var <- function (object, ...)
- stop("function ",sQuote("pred.var")," is undefined for objects of class ",sQuote(class(object)))
-setGeneric('pred.var')
-
-filter.mean <- function (object, ...)
- stop("function ",sQuote("filter.mean")," is undefined for objects of class ",sQuote(class(object)))
-setGeneric('filter.mean')
-
conv.rec <- function (object, ...)
stop("function ",sQuote("conv.rec")," is undefined for objects of class ",sQuote(class(object)))
setGeneric('conv.rec')
@@ -19,37 +7,6 @@
## extract the estimated log likelihood
setMethod('logLik','mif',function(object,...)object at loglik)
-## extract the prediction means
-setMethod(
- 'pred.mean',
- 'mif',
- function (object, pars, ...) {
- if (missing(pars)) pars <- rownames(object at pred.mean)
- object at pred.mean[pars,]
- }
- )
-
-## extract the prediction variances
-setMethod(
- 'pred.var',
- 'mif',
- function (object, pars, ...) {
- if (missing(pars)) pars <- rownames(object at pred.var)
- object at pred.var[pars,]
- }
- )
-
-
-## extract the filtering means
-setMethod(
- 'filter.mean',
- 'mif',
- function (object, pars, ...) {
- if (missing(pars)) pars <- rownames(object at filter.mean)
- object at filter.mean[pars,]
- }
- )
-
## extract the convergence record
setMethod(
'conv.rec',
Added: pkg/R/pfilter-methods.R
===================================================================
--- pkg/R/pfilter-methods.R (rev 0)
+++ pkg/R/pfilter-methods.R 2011-05-04 21:33:27 UTC (rev 456)
@@ -0,0 +1,34 @@
+setMethod("$",signature(x="pfilterd.pomp"),function (x,name) slot(x,name))
+setMethod("logLik",signature(object="pfilterd.pomp"),function(object,...)object at loglik)
+
+## extract the prediction means
+setMethod(
+ "pred.mean",
+ "pfilterd.pomp",
+ function (object, pars, ...) {
+ if (missing(pars)) pars <- rownames(object at pred.mean)
+ object at pred.mean[pars,]
+ }
+ )
+
+## extract the prediction variances
+setMethod(
+ "pred.var",
+ "pfilterd.pomp",
+ function (object, pars, ...) {
+ if (missing(pars)) pars <- rownames(object at pred.var)
+ object at pred.var[pars,]
+ }
+ )
+
+
+## extract the filtering means
+setMethod(
+ "filter.mean",
+ "pfilterd.pomp",
+ function (object, pars, ...) {
+ if (missing(pars)) pars <- rownames(object at filter.mean)
+ object at filter.mean[pars,]
+ }
+ )
+
Modified: pkg/R/pfilter.R
===================================================================
--- pkg/R/pfilter.R 2011-05-04 21:32:39 UTC (rev 455)
+++ pkg/R/pfilter.R 2011-05-04 21:33:27 UTC (rev 456)
@@ -322,6 +322,3 @@
}
)
-setMethod("$",signature(x="pfilterd.pomp"),function (x,name) slot(x,name))
-setMethod("logLik",signature(object="pfilterd.pomp"),function(object,...)object at loglik)
-
Modified: pkg/man/mif-methods.Rd
===================================================================
--- pkg/man/mif-methods.Rd 2011-05-04 21:32:39 UTC (rev 455)
+++ pkg/man/mif-methods.Rd 2011-05-04 21:33:27 UTC (rev 456)
@@ -6,15 +6,6 @@
\alias{conv.rec}
\alias{conv.rec,mif-method}
\alias{conv.rec-mif}
-\alias{pred.mean}
-\alias{pred.mean,mif-method}
-\alias{pred.mean-mif}
-\alias{pred.var}
-\alias{pred.var,mif-method}
-\alias{pred.var-mif}
-\alias{filter.mean}
-\alias{filter.mean,mif-method}
-\alias{filter.mean-mif}
\alias{plot-mif}
\alias{plot,mif-method}
\alias{compare.mif}
@@ -23,9 +14,6 @@
\usage{
\S4method{logLik}{mif}(object, \dots)
\S4method{conv.rec}{mif}(object, pars, \dots)
-\S4method{pred.mean}{mif}(object, pars, \dots)
-\S4method{pred.var}{mif}(object, pars, \dots)
-\S4method{filter.mean}{mif}(object, pars, \dots)
\S4method{plot}{mif}(x, y = NULL, \dots)
compare.mif(z)
}
@@ -59,18 +47,6 @@
Plots a series of diagnostic plots.
When \code{x} is a \code{mif} object, \code{plot(x)} is equivalent to \code{compare.mif(list(x))}.
}
- \item{pred.mean}{
- \code{pred.mean(object, pars = NULL)} returns the rows of the prediction-mean matrix corresponding to the names in \code{pars}.
- By default, all rows are returned.
- }
- \item{pred.var}{
- \code{pred.var(object, pars = NULL)} returns the rows of the prediction-variance matrix corresponding to the names in \code{pars}.
- By default, all rows are returned.
- }
- \item{filter.mean}{
- \code{filter.mean(object, pars = NULL)} returns the rows of the filtering-mean matrix corresponding to the names in \code{pars}.
- By default, all rows are returned.
- }
\item{predvarplot}{
\code{predvarplot(object, pars = NULL, mean = FALSE, \dots)} produces a plot of the scaled prediction variances for each parameter.
This can be used to diagnose a good value of the \code{mif} parameters \code{var.factor} and \code{ic.lag}.
Added: pkg/man/pfilter-methods.Rd
===================================================================
--- pkg/man/pfilter-methods.Rd (rev 0)
+++ pkg/man/pfilter-methods.Rd 2011-05-04 21:33:27 UTC (rev 456)
@@ -0,0 +1,35 @@
+\name{pfilter-methods}
+\alias{logLik,pfilterd.pomp-method}
+\alias{logLik-pfilterd.pomp}
+\alias{$,pfilterd.pomp-method}
+\alias{$-pfilterd.pomp}
+\alias{pred.mean}
+\alias{pred.mean,pfilterd.pomp-method}
+\alias{pred.mean-pfilterd.pomp}
+\alias{pred.var}
+\alias{pred.var,pfilterd.pomp-method}
+\alias{pred.var-pfilterd.pomp}
+\alias{filter.mean}
+\alias{filter.mean,pfilterd.pomp-method}
+\alias{filter.mean-pfilterd.pomp}
+\title{Methods of the "pfilterd.pomp" class}
+\description{Methods of the "pfilterd.pomp" class.}
+\usage{
+\S4method{logLik}{pfilterd.pomp}(object, \dots)
+\S4method{pred.mean}{pfilterd.pomp}(object, pars, \dots)
+\S4method{pred.var}{pfilterd.pomp}(object, pars, \dots)
+\S4method{filter.mean}{pfilterd.pomp}(object, pars, \dots)
+}
+\arguments{
+ \item{object}{
+ An object of class \code{pfilterd.pomp} or inheriting class \code{pfilterd.pomp}.
+ }
+ \item{pars}{Names of parameters.}
+ \item{\dots}{
+ Additional arguments unused at present.
+ }
+}
+\author{Aaron A. King \email{kingaa at umich dot edu}}
+\seealso{\code{\link{pfilter}}, \link{pomp-class}}
+\keyword{models}
+\keyword{ts}
Modified: pkg/man/pfilter.Rd
===================================================================
--- pkg/man/pfilter.Rd 2011-05-04 21:32:39 UTC (rev 455)
+++ pkg/man/pfilter.Rd 2011-05-04 21:33:27 UTC (rev 456)
@@ -4,10 +4,6 @@
\alias{pfilter-pomp}
\alias{pfilter,pfilterd.pomp-method}
\alias{pfilter-pfilterd.pomp}
-\alias{logLik,pfilterd.pomp-method}
-\alias{logLik-pfilterd.pomp}
-\alias{$,pfilterd.pomp-method}
-\alias{$-pfilterd.pomp}
\alias{pfilterd.pomp-class}
\title{Particle filter}
\description{
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