[Pomp-commits] r927 - in pkg/mif2: . man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Apr 18 13:24:16 CEST 2014
Author: kingaa
Date: 2014-04-18 13:24:16 +0200 (Fri, 18 Apr 2014)
New Revision: 927
Added:
pkg/mif2/man/mif2-class.Rd
pkg/mif2/man/mif2-methods.Rd
Modified:
pkg/mif2/DESCRIPTION
pkg/mif2/man/mif2.Rd
Log:
- fix some documentation problems
Modified: pkg/mif2/DESCRIPTION
===================================================================
--- pkg/mif2/DESCRIPTION 2014-04-17 17:30:38 UTC (rev 926)
+++ pkg/mif2/DESCRIPTION 2014-04-18 11:24:16 UTC (rev 927)
@@ -1,8 +1,8 @@
Package: mif2
Type: Package
Title: Statistical inference for partially observed Markov processes
-Version: 0.50-1
-Date: 2014-04-17
+Version: 1.0-1
+Date: 2014-04-18
Authors at R: c(person(given=c("Aaron","A."),family="King",
role=c("aut","cre"),email="kingaa at umich.edu"),
person(given=c("Edward","L."),family="Ionides",role=c("aut")),
Added: pkg/mif2/man/mif2-class.Rd
===================================================================
--- pkg/mif2/man/mif2-class.Rd (rev 0)
+++ pkg/mif2/man/mif2-class.Rd 2014-04-18 11:24:16 UTC (rev 927)
@@ -0,0 +1,51 @@
+\name{mif2d.pomp-class}
+\docType{class}
+\alias{mif2d.pomp-class}
+\keyword{internal}
+\title{The "mif2d.pomp" class}
+\description{
+ The \code{mif2d.pomp} class holds a fitted model and is created by a call to \code{\link{mif2}}.
+ See \code{\link{mif2}} for usage.
+}
+\section{Objects from the Class}{
+ Objects can be created by calls to the \code{\link{mif2}} method on a \code{\link{pomp}} or \code{\link[pomp]{pfilterd.pomp-class}} object.
+ Such a call uses the MIF2 algorithm to fit the model parameters.
+}
+\section{Slots}{
+ A \code{mif2d.pomp} object is derived from a \code{pfilterd.pomp} object and therefore has all the slots of such an object.
+ The \code{mif2d.pomp} specific slots are described below.
+ \describe{
+ \item{transform}{
+ logical scalar; was the estimation done on the transformed scale?
+ }
+ \item{Nmif}{
+ integer; number of MIF2 iterations that have been completed.
+ }
+ \item{perturb.fn}{
+ function.
+ }
+ \item{conv.rec}{
+ The \dQuote{convergence record}: a matrix containing a record of the parameter values, log likelihoods, and other pertinent information, with one row for each MIF2 iteration.
+ }
+ \item{pred.mean, pred.var, filter.mean,
+ eff.sample.size, cond.loglik, saved.states, saved.params, seed,
+ Np, tol, nfail, loglik,
+ data, times, t0, rprocess, dprocess, dmeasure, rmeasure,
+ skeleton.type, skeleton, initializer, states, params,
+ statenames, paramnames, covarnames, obsnames, tcovar, covar,
+ PACKAGE, userdata}{
+ Inherited from the \code{pfilterd.pomp} class.
+ }
+ }
+}
+\section{Extends}{
+ Class \code{pfilterd.pomp}, directly.
+ See \code{\link{pfilter}}.
+}
+\section{Methods}{
+ See \code{\link{mif2}}, \link{mif2-methods}.
+}
+\author{Aaron A. King \email{kingaa at umich dot edu}}
+\seealso{\code{\link[pomp]{mif}}, \link{mif2-methods}, \code{\link[pomp]{pomp}}, \link[pomp]{pomp-class}}
+\keyword{models}
+\keyword{ts}
Added: pkg/mif2/man/mif2-methods.Rd
===================================================================
--- pkg/mif2/man/mif2-methods.Rd (rev 0)
+++ pkg/mif2/man/mif2-methods.Rd 2014-04-18 11:24:16 UTC (rev 927)
@@ -0,0 +1,56 @@
+\name{mif2-methods}
+\docType{methods}
+\alias{mif2-methods}
+\alias{logLik,mif2d.pomp-method}
+\alias{logLik-mif2d.pomp}
+\alias{conv.rec,mif2d.pomp-method}
+\alias{conv.rec-mif2d.pomp}
+\alias{plot-mif2d.pomp}
+\alias{plot,mif2d.pomp-method}
+\title{Methods of the "mif2d.class" class}
+\description{Methods of the \code{mif2d.class} class.}
+\usage{
+\S4method{logLik}{mif2d.pomp}(object, \dots)
+\S4method{conv.rec}{mif2d.pomp}(object, pars, transform = FALSE, \dots)
+\S4method{plot}{mif2d.pomp}(x, y = NULL, \dots)
+}
+\arguments{
+ \item{object, x}{The \code{mif2d.pomp} object.}
+ \item{pars}{Names of parameters.}
+ \item{y}{Ignored.}
+ \item{transform}{
+ optional logical;
+ should the parameter transformations be applied?
+ See \code{\link[=coef-pomp]{coef}} for details.
+ }
+ \item{\dots}{
+ Further arguments (either ignored or passed to underlying functions).
+ }
+}
+\section{Methods}{
+ \describe{
+ \item{conv.rec}{
+ \code{conv.rec(object, pars = NULL)} returns the columns of the convergence-record matrix corresponding to the names in \code{pars}.
+ By default, all rows are returned.
+ }
+ \item{logLik}{
+ Returns the value in the \code{loglik} slot.
+ }
+ \item{plot}{
+ Plots a series of diagnostic plots.
+ }
+ }
+}
+\references{
+ E. L. Ionides, C. Bret\\'o, & A. A. King,
+ Inference for nonlinear dynamical systems,
+ Proc. Natl. Acad. Sci. U.S.A., 103:18438--18443, 2006.
+
+ A. A. King, E. L. Ionides, M. Pascual, and M. J. Bouma,
+ Inapparent infections and cholera dynamics,
+ Nature, 454:877--880, 2008.
+}
+\author{Aaron A. King \email{kingaa at umich dot edu}}
+\seealso{\code{\link{mif}}, \code{\link{pomp}}, \code{\link{pomp-class}}, \code{\link{pfilter}}}
+\keyword{models}
+\keyword{ts}
Modified: pkg/mif2/man/mif2.Rd
===================================================================
--- pkg/mif2/man/mif2.Rd 2014-04-17 17:30:38 UTC (rev 926)
+++ pkg/mif2/man/mif2.Rd 2014-04-18 11:24:16 UTC (rev 927)
@@ -44,7 +44,7 @@
\code{Np(T)} is the number of particles to sample at the end of the time-series.
}
\item{perturb.fn}{
- \code(perturb.fn(params,mifiter,timeno,\dots))
+ \code{perturb.fn(params,mifiter,timeno,\dots)}
}
\item{tol}{
See the description under \code{\link{pfilter}}.
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