[Pomp-commits] r1109 - pkg/pomp/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Feb 27 03:58:04 CET 2015
Author: kingaa
Date: 2015-02-27 03:58:03 +0100 (Fri, 27 Feb 2015)
New Revision: 1109
Removed:
pkg/pomp/man/pmcmc-methods.Rd
pkg/pomp/man/probed-pomp-methods.Rd
Modified:
pkg/pomp/man/basic-probes.Rd
pkg/pomp/man/csnippet.Rd
pkg/pomp/man/eulermultinom.Rd
pkg/pomp/man/pmcmc.Rd
pkg/pomp/man/pomp-methods.Rd
pkg/pomp/man/pomp.Rd
pkg/pomp/man/probe.Rd
pkg/pomp/man/spect.Rd
Log:
- more work on the help pages
Modified: pkg/pomp/man/basic-probes.Rd
===================================================================
--- pkg/pomp/man/basic-probes.Rd 2015-02-27 02:58:00 UTC (rev 1108)
+++ pkg/pomp/man/basic-probes.Rd 2015-02-27 02:58:03 UTC (rev 1109)
@@ -1,4 +1,6 @@
-\name{basic.probes}
+\name{Probe functions}
+\title{Some useful probes for partially-observed Markov processes}
+\alias{Probe functions}
\alias{basic.probes}
\alias{probe.mean}
\alias{probe.median}
@@ -10,10 +12,9 @@
\alias{probe.ccf}
\alias{probe.marginal}
\alias{probe.nlar}
-\title{Some probes for partially-observed Markov processes}
\description{
- Several simple and configurable probes are provided in the package.
- These can be used directly and as examples for building custom probes.
+ Several simple and configurable probes are provided with in the package.
+ These can be used directly and as templates for custom probes.
}
\usage{
probe.mean(var, trim = 0, transform = identity, na.rm = TRUE)
Modified: pkg/pomp/man/csnippet.Rd
===================================================================
--- pkg/pomp/man/csnippet.Rd 2015-02-27 02:58:00 UTC (rev 1108)
+++ pkg/pomp/man/csnippet.Rd 2015-02-27 02:58:03 UTC (rev 1109)
@@ -1,7 +1,7 @@
\name{Csnippet}
+\title{C code snippets for accelerating computations}
\alias{Csnippet}
\alias{Csnippet-class}
-\title{C code snippets}
\description{
For including snippets of C code in \code{pomp} objects.
}
@@ -10,12 +10,21 @@
}
\arguments{
\item{text}{
- character; a snippt of C code.
+ character; a snippet of C code.
}
}
\value{
An object of class \code{Csnippet}.
}
+\section{Using C snippets to accelerate computations}{
+ From version 0.50, \pkg{pomp} provides a facility whereby users can define their model's components using inline C code.
+ The \code{pomp} constructor combines these \code{Csnippet}s into a compilable C file stored in the \R session's temporary directory.
+ They are then compiled (via \code{\link[=SHLIB]{R CMD SHLIB}}) into dynamically loadable shared objects.
+ This is then dynamically loaded as needed.
+}
\author{Aaron A. King \email{kingaa at umich dot edu}}
+\seealso{
+ \code{\link{pomp}}, \code{\link{plugins}}, and the tutorials on the \href{http://pomp.r-forge.r-project.org}{package website}.
+}
\keyword{programming}
\keyword{interface}
Modified: pkg/pomp/man/eulermultinom.Rd
===================================================================
--- pkg/pomp/man/eulermultinom.Rd 2015-02-27 02:58:00 UTC (rev 1108)
+++ pkg/pomp/man/eulermultinom.Rd 2015-02-27 02:58:03 UTC (rev 1109)
@@ -1,11 +1,11 @@
\name{eulermultinom}
+\title{The Euler-multinomial distributions and Gamma white-noise processes}
\alias{eulermultinom}
\alias{reulermultinom}
\alias{deulermultinom}
\alias{rgammawn}
-\title{Euler-multinomial death process}
\description{
- Density and random-deviate generation for the Euler-multinomial death process with parameters \code{size}, \code{rate}, and \code{dt}.
+ This page documents both the Euler-multinomial family of distributions and the package's simulator of Gamma white-noise processes.
}
\usage{
reulermultinom(n = 1, size, rate, dt)
@@ -75,6 +75,10 @@
Returns a vector of length \code{n} containing random increments of the integrated Gamma white noise process with intensity \code{sigma}.
}
}
+\section{C interface}{
+ A C API for these functions is also provided by the package.
+ At an \R prompt, execute \preformatted{file.show(system.file("include/pomp.h",package="pomp"))} to view the header file that defines and explains the API.
+}
\author{Aaron A. King \email{kingaa at umich dot edu}}
\examples{
print(dn <- reulermultinom(5,size=100,rate=c(a=1,b=2,c=3),dt=0.1))
@@ -92,5 +96,5 @@
D. He, E. L. Ionides, & A. A. King,
Plug-and-play inference for disease dynamics: measles in large and small populations as a case study.
J. R. Soc. Interface, 7:271--283, 2010.
- }
+}
\keyword{distribution}
Deleted: pkg/pomp/man/pmcmc-methods.Rd
===================================================================
--- pkg/pomp/man/pmcmc-methods.Rd 2015-02-27 02:58:00 UTC (rev 1108)
+++ pkg/pomp/man/pmcmc-methods.Rd 2015-02-27 02:58:03 UTC (rev 1109)
@@ -1,68 +0,0 @@
-\name{pmcmc-methods}
-\docType{methods}
-\alias{pmcmc-methods}
-\alias{logLik,pmcmc-method}
-\alias{logLik-pmcmc}
-\alias{conv.rec,pmcmc-method}
-\alias{conv.rec-pmcmc}
-\alias{conv.rec,pmcmcList-method}
-\alias{conv.rec-pmcmcList}
-\alias{plot-pmcmc}
-\alias{plot,pmcmc-method}
-\alias{plot-pmcmcList}
-\alias{plot,pmcmcList-method}
-\alias{pmcmcList-class}
-\alias{c-pmcmc}
-\alias{c,pmcmc-method}
-\alias{c-pmcmcList}
-\alias{c,pmcmcList-method}
-\alias{[-pmcmcList}
-\alias{[,pmcmcList-method}
-\title{Methods of the "pmcmc" class}
-\description{Methods of the "pmcmc" class.}
-\usage{
-\S4method{logLik}{pmcmc}(object, \dots)
-\S4method{conv.rec}{pmcmc}(object, pars, \dots)
-\S4method{conv.rec}{pmcmcList}(object, \dots)
-\S4method{plot}{pmcmc}(x, y, \dots)
-\S4method{plot}{pmcmcList}(x, y, \dots)
-\S4method{c}{pmcmc}(x, \dots, recursive = FALSE)
-\S4method{c}{pmcmcList}(x, \dots, recursive = FALSE)
-}
-\arguments{
- \item{object, x}{The \code{pmcmc} or \code{pmcmcList} object.}
- \item{pars}{Names of parameters.}
- \item{y, recursive}{Ignored.}
- \item{\dots}{
- Further arguments (either ignored or passed to underlying functions).
- }
-}
-\section{Methods}{
- \describe{
- \item{conv.rec}{
- \code{conv.rec(object, pars)} returns the columns of the convergence-record matrix corresponding to the names in \code{pars} as an object of class \code{\link[coda]{mcmc}} or \code{\link[coda]{mcmc.list}}.
- }
- \item{plot}{
- Diagnostic plots.
- }
- \item{logLik}{
- Returns the value in the \code{loglik} slot.
- }
- \item{c}{
- Concatenates \code{pmcmc} objects into a \code{pmcmcList}.
- }
- }
-}
-\references{
- C. Andrieu, A. Doucet and R. Holenstein,
- Particle Markov chain Monte Carlo methods,
- J. Roy. Stat. Soc B, to appear, 2010.
-
- C. Andrieu and G.O. Roberts,
- The pseudo-marginal approach for efficient computation,
- Ann Stat 37:697-725, 2009.
-}
-\author{Edward L. Ionides \email{ionides at umich dot edu}, Aaron A. King \email{kingaa at umich dot edu}}
-\seealso{\code{\link{pmcmc}}, \code{\link{pomp}}, \code{\link{pomp-class}}, \code{\link{pfilter}}}
-\keyword{models}
-\keyword{ts}
Modified: pkg/pomp/man/pmcmc.Rd
===================================================================
--- pkg/pomp/man/pmcmc.Rd 2015-02-27 02:58:00 UTC (rev 1108)
+++ pkg/pomp/man/pmcmc.Rd 2015-02-27 02:58:03 UTC (rev 1109)
@@ -1,4 +1,5 @@
-\name{pmcmc}
+\name{Particle Markov Chain Monte Carlo}
+\title{The particle Markov chain Metropolis-Hastings algorithm}
\docType{methods}
\alias{pmcmc}
\alias{pmcmc,pmcmc-method}
@@ -10,7 +11,24 @@
\alias{continue,pmcmc-method}
\alias{continue-pmcmc}
\alias{pmcmc-class}
-\title{The PMCMC algorithm}
+\alias{pmcmc-methods}
+\alias{logLik,pmcmc-method}
+\alias{logLik-pmcmc}
+\alias{conv.rec,pmcmc-method}
+\alias{conv.rec-pmcmc}
+\alias{conv.rec,pmcmcList-method}
+\alias{conv.rec-pmcmcList}
+\alias{plot-pmcmc}
+\alias{plot,pmcmc-method}
+\alias{plot-pmcmcList}
+\alias{plot,pmcmcList-method}
+\alias{pmcmcList-class}
+\alias{c-pmcmc}
+\alias{c,pmcmc-method}
+\alias{c-pmcmcList}
+\alias{c,pmcmcList-method}
+\alias{[-pmcmcList}
+\alias{[,pmcmcList-method}
\description{
The Particle MCMC algorithm for estimating the parameters of a partially-observed Markov process.
}
@@ -80,6 +98,22 @@
This gives an asymptotically correct Bayesian procedure for parameter estimation (Andrieu and Roberts, 2009).
An extension to give a correct Bayesian posterior distribution of unobserved state variables (as in Andrieu et al, 2010) has not yet been implemented.
}
+\section{Methods}{
+ \describe{
+ \item{conv.rec}{
+ \code{conv.rec(object, pars)} returns the columns of the convergence-record matrix corresponding to the names in \code{pars} as an object of class \code{\link[coda]{mcmc}} or \code{\link[coda]{mcmc.list}}.
+ }
+ \item{plot}{
+ Diagnostic plots.
+ }
+ \item{logLik}{
+ Returns the value in the \code{loglik} slot.
+ }
+ \item{c}{
+ Concatenates \code{pmcmc} objects into a \code{pmcmcList}.
+ }
+ }
+}
\references{
C. Andrieu, A. Doucet and R. Holenstein,
Particle Markov chain Monte Carlo methods,
@@ -91,6 +125,7 @@
}
\author{Edward L. Ionides \email{ionides at umich dot edu}, Aaron A. King \email{kingaa at umich dot edu}}
\seealso{
- \code{\link{pmcmc-class}}, \code{\link{pmcmc-methods}}, \code{\link{pomp}}, \code{\link{pomp-class}}, \code{\link{pfilter}}.
+ \code{\link{pomp}}, \code{\link{pfilter}},
+ and the tutorials on the \href{http://pomp.r-forge.r-project.org}{package website}.
}
\keyword{ts}
Modified: pkg/pomp/man/pomp-methods.Rd
===================================================================
--- pkg/pomp/man/pomp-methods.Rd 2015-02-27 02:58:00 UTC (rev 1108)
+++ pkg/pomp/man/pomp-methods.Rd 2015-02-27 02:58:03 UTC (rev 1109)
@@ -1,4 +1,4 @@
-\name{pomp-methods}
+\name{pomp methods}
\docType{methods}
\alias{pomp methods}
\alias{pomp-methods}
@@ -41,10 +41,9 @@
\alias{coef<-}
\alias{coef<-,pomp-method}
\alias{coef<--pomp}
-\title{Methods of the "pomp" class}
-\description{Methods of the \code{pomp} class.}
+\title{Functions for manipulating, displaying, and extracting information from objects of the \code{pomp} class}
+\description{This page documents the various methods that allow one to extract information from, display, plot, and modify \code{pomp} objects.}
\usage{
-\S3method{as.data.frame}{pomp}(x, row.names, optional, \dots)
\S4method{coef}{pomp}(object, pars, transform = FALSE, \dots)
\S4method{coef}{pomp}(object, pars, transform = FALSE, \dots) <- value
\S4method{obs}{pomp}(object, vars, \dots)
@@ -62,7 +61,6 @@
\S4method{timezero}{pomp}(object, \dots) <- value
\S4method{window}{pomp}(x, start, end, \dots)
\S4method{as}{pomp}(object, class)
-\S4method{coerce}{pomp,data.frame}(from, to = "data.frame", strict = TRUE)
}
\arguments{
\item{object, x}{The \code{pomp} object.}
@@ -104,12 +102,6 @@
character;
name of the class to which \code{object} should be coerced.
}
- \item{from, to}{
- the classes between which coercion should be performed.
- }
- \item{strict}{
- ignored.
- }
\item{y}{ignored.}
\item{variables}{
optional character;
@@ -134,9 +126,6 @@
logical;
indicates if x- and y- axes should be drawn.
}
- \item{row.names, optional}{
- ignored.
- }
\item{\dots}{
Further arguments (either ignored or passed to underlying functions).
}
Modified: pkg/pomp/man/pomp.Rd
===================================================================
--- pkg/pomp/man/pomp.Rd 2015-02-27 02:58:00 UTC (rev 1108)
+++ pkg/pomp/man/pomp.Rd 2015-02-27 02:58:03 UTC (rev 1109)
@@ -344,5 +344,6 @@
\link{process model plugins}
}
\keyword{models}
+\keyword{interface}
+\keyword{programming}
\keyword{ts}
-
Modified: pkg/pomp/man/probe.Rd
===================================================================
--- pkg/pomp/man/probe.Rd 2015-02-27 02:58:00 UTC (rev 1108)
+++ pkg/pomp/man/probe.Rd 2015-02-27 02:58:03 UTC (rev 1109)
@@ -1,4 +1,5 @@
\name{probe}
+\title{Probe a partially-observed Markov process by computing summary statistics and the synthetic likelihood.}
\alias{probe}
\alias{probe,pomp-method}
\alias{probe,probed.pomp-method}
@@ -18,7 +19,39 @@
\alias{probe.match.objfun,probed.pomp-method}
\alias{probe.match.objfun-pomp}
\alias{probe.match.objfun-probed.pomp}
-\title{Probe a partially-observed Markov process.}
+\alias{probed.pomp-methods}
+\alias{probe.matched.pomp-methods}
+\alias{spect.pomp-methods}
+\alias{spect.matched.pomp-methods}
+\alias{summary,probed.pomp-method}
+\alias{summary,probe.matched.pomp-method}
+\alias{summary-probed.pomp}
+\alias{summary-probe.matched.pomp}
+\alias{values}
+\alias{values,probed.pomp-method}
+\alias{values,probe.matched.pomp-method}
+\alias{values-probed.pomp}
+\alias{values-probe.matched.pomp}
+\alias{plot,probed.pomp-method}
+\alias{plot,probe.matched.pomp-method}
+\alias{plot-probed.pomp}
+\alias{plot-probe.matched.pomp}
+\alias{summary,spect.pomp-method}
+\alias{summary,spect.matched.pomp-method}
+\alias{summary-spect.pomp}
+\alias{summary-spect.matched.pomp}
+\alias{plot,spect.pomp-method}
+\alias{plot,spect.matched.pomp-method}
+\alias{plot,spect.pomp-method}
+\alias{plot-spect.pomp}
+\alias{as,probed.pomp-method}
+\alias{logLik,probed.pomp-method}
+\alias{logLik-probed.pomp}
+\alias{$,probed.pomp-method}
+\alias{$-probed.pomp}
+\alias{$,probe.matched.pomp-method}
+\alias{$-probe.matched.pomp}
+\alias{coerce,probed.pomp,data.frame-method}
\description{
\code{probe} applies one or more \dQuote{probes} to time series data and model simulations and compares the results.
It can be used to diagnose goodness of fit and/or as the basis for \dQuote{probe-matching}, a generalized method-of-moments approach to parameter estimation.
@@ -43,6 +76,8 @@
\S4method{probe.match}{probe.matched.pomp}(object, est, probes,
nsim, seed, transform, fail.value, \dots,
verbose = getOption("verbose"))
+\S4method{logLik}{probed.pomp}(object, \dots)
+\S4method{values}{probed.pomp}(object, \dots)
}
\arguments{
\item{object}{
@@ -52,7 +87,7 @@
A single probe or a list of one or more probes.
A probe is simply a scalar- or vector-valued function of one argument that can be applied to the data array of a \code{pomp}.
A vector-valued probe must always return a vector of the same size.
- A number of basic examples are provided with the package (see \link{basic.probes}).
+ A number of useful examples are provided with the package: see \link{Probe functions}).
}
\item{params}{
optional named numeric vector of model parameters.
@@ -141,6 +176,29 @@
\code{probe.match.objfun} returns a function suitable for use as an objective function in an \code{\link{optim}}-like optimizer.
}
+\section{Methods}{
+ \describe{
+ \item{plot}{
+ displays diagnostic plots.
+ }
+ \item{summary}{
+ displays summary information.
+ }
+ \item{values}{
+ extracts the realized values of the probes on the data and on the simulations as a data frame in long format.
+ The variable \code{.id} indicates whether the probes are from the data or simulations.
+ }
+ \item{logLik}{
+ returns the synthetic likelihood for the probes.
+ NB: in general, this is not the same as the likelihood.
+ }
+ \item{as, as.data.frame}{
+ when a \sQuote{probed.pomp} is coerced to a \sQuote{data.frame}, the first row gives the probes applied to the data; the rest of the rows give the probes evaluated on simulated data.
+ The rownames of the result can be used to distinguish these.
+ }
+ }
+ In addition, slots of this object can be accessed via the \code{$} operator.
+}
\references{
B. E. Kendall, C. J. Briggs, W. M. Murdoch, P. Turchin, S. P. Ellner, E. McCauley, R. M. Nisbet, S. N. Wood
Why do populations cycle? A synthesis of statistical and mechanistic modeling approaches,
@@ -188,14 +246,8 @@
plot(bad)
}
\seealso{
- \link{pomp-class},
- \link{pomp-methods},
- \link{basic.probes},
- \code{\link{probe.match}}
+ \link{pomp}, \link{Probe functions}, \link{spect},
+ and the tutorials on the \href{http://pomp.r-forge.r-project.org}{package website}.
}
\keyword{models}
\keyword{ts}
-
-
-
-
Deleted: pkg/pomp/man/probed-pomp-methods.Rd
===================================================================
--- pkg/pomp/man/probed-pomp-methods.Rd 2015-02-27 02:58:00 UTC (rev 1108)
+++ pkg/pomp/man/probed-pomp-methods.Rd 2015-02-27 02:58:03 UTC (rev 1109)
@@ -1,106 +0,0 @@
-\name{probed.pomp-methods}
-\docType{methods}
-\alias{probed.pomp-methods}
-\alias{probe.matched.pomp-methods}
-\alias{spect.pomp-methods}
-\alias{spect.matched.pomp-methods}
-\alias{summary,probed.pomp-method}
-\alias{summary,probe.matched.pomp-method}
-\alias{summary-probed.pomp}
-\alias{summary-probe.matched.pomp}
-\alias{values}
-\alias{values,probed.pomp-method}
-\alias{values,probe.matched.pomp-method}
-\alias{values-probed.pomp}
-\alias{values-probe.matched.pomp}
-\alias{plot,probed.pomp-method}
-\alias{plot,probe.matched.pomp-method}
-\alias{plot-probed.pomp}
-\alias{plot-probe.matched.pomp}
-\alias{summary,spect.pomp-method}
-\alias{summary,spect.matched.pomp-method}
-\alias{summary-spect.pomp}
-\alias{summary-spect.matched.pomp}
-\alias{plot,spect.pomp-method}
-\alias{plot,spect.matched.pomp-method}
-\alias{plot,spect.pomp-method}
-\alias{plot-spect.pomp}
-\alias{as,probed.pomp-method}
-\alias{logLik,probed.pomp-method}
-\alias{logLik-probed.pomp}
-\alias{$,probed.pomp-method}
-\alias{$-probed.pomp}
-\alias{$,probe.matched.pomp-method}
-\alias{$-probe.matched.pomp}
-\alias{coerce,probed.pomp,data.frame-method}
-\title{Methods of the "probed.pomp", "probe.matched.pomp", "spect.pomp", and "spect.matched.pomp" classes}
-\description{Methods of the \code{probed.pomp}, \code{probe.matched.pomp}, \code{spect.pomp}, and \code{spect.matched.pomp} classes}
-\usage{
-\S4method{summary}{probed.pomp}(object, \dots)
-\S4method{plot}{probed.pomp}(x, y, \dots)
-\S4method{summary}{probe.matched.pomp}(object, \dots)
-\S4method{plot}{probe.matched.pomp}(x, y, \dots)
-\S4method{summary}{spect.pomp}(object, \dots)
-\S4method{logLik}{probed.pomp}(object, \dots)
-\S4method{values}{probed.pomp}(object, \dots)
-\S4method{plot}{spect.pomp}(x, y, max.plots.per.page = 4,
- plot.data = TRUE,
- quantiles = c(.025, .25, .5, .75, .975),
- quantile.styles = list(lwd=1, lty=1, col="gray70"),
- data.styles = list(lwd=2, lty=2, col="black"))
-\S4method{summary}{spect.matched.pomp}(object, \dots)
-\S4method{plot}{spect.matched.pomp}(x, y, \dots)
-\S4method{as}{probed.pomp}(object, class)
-}
-\arguments{
- \item{object, x}{the object to be summarized or plotted.}
- \item{y}{ignored.}
- \item{max.plots.per.page}{maximum number of plots per page}
- \item{plot.data}{plot the data spectrum?}
- \item{quantiles}{quantiles to plot}
- \item{quantile.styles}{plot style parameters for the quantiles}
- \item{data.styles}{plot style parameters for the data spectrum}
- \item{class}{
- character;
- name of the class to which \code{object} should be coerced.
- }
- \item{\dots}{
- Further arguments (either ignored or passed to underlying functions).
- }
-}
-\section{Methods}{
- \describe{
- \item{plot}{
- displays diagnostic plots.
- }
- \item{summary}{
- displays summary information.
- }
- \item{values}{
- extracts the realized values of the probes on the data and on the simulations as a data frame in long format.
- The variable \code{.id} indicates whether the probes are from the data or simulations.
- }
- \item{logLik}{
- returns the synthetic likelihood for the probes.
- NB: in general, this is not the same as the likelihood.
- }
- \item{as}{
- when a \sQuote{probed.pomp} is coerced to a \sQuote{data.frame}, the first row gives the probes applied to the data; the rest of the rows give the probes evaluated on simulated data.
- The rownames of the result can be used to distinguish these.
- }
- }
-
- In addition, slots of this object can be accessed via the \code{$} operator.
-
-}
-\author{
- Daniel C. Reuman, Aaron A. King
-}
-\seealso{
- \code{\link{probe}},
- \code{\link[=probed.pomp-class]{probed.pomp}},
- \code{\link[=probe.matched.pomp-class]{probe.matched.pomp}},
- \code{\link{probe.match}}
-}
-\keyword{models}
-\keyword{ts}
Modified: pkg/pomp/man/spect.Rd
===================================================================
--- pkg/pomp/man/spect.Rd 2015-02-27 02:58:00 UTC (rev 1108)
+++ pkg/pomp/man/spect.Rd 2015-02-27 02:58:03 UTC (rev 1109)
@@ -174,10 +174,7 @@
plot(bad)
}
\seealso{
- \link{pomp-class},
- \link{pomp-methods},
- \code{\link{probe}},
- \code{\link{probe.match}}
+ \link{pomp}, \code{\link{probe}}
}
\keyword{models}
\keyword{ts}
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