[Pomp-commits] r950 - in pkg/pomp: . R inst inst/doc man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri May 16 18:39:56 CEST 2014
Author: kingaa
Date: 2014-05-16 18:39:56 +0200 (Fri, 16 May 2014)
New Revision: 950
Removed:
pkg/pomp/inst/doc/advanced_topics_in_pomp.pdf
pkg/pomp/inst/doc/intro_to_pomp.pdf
pkg/pomp/inst/doc/manual.pdf
Modified:
pkg/pomp/DESCRIPTION
pkg/pomp/R/builder.R
pkg/pomp/inst/NEWS
pkg/pomp/inst/NEWS.Rd
pkg/pomp/inst/doc/index.html
pkg/pomp/man/basic-probes.Rd
pkg/pomp/man/blowflies.Rd
pkg/pomp/man/bsmc.Rd
pkg/pomp/man/builder.Rd
pkg/pomp/man/mif-methods.Rd
pkg/pomp/man/mif.Rd
pkg/pomp/man/nlf.Rd
pkg/pomp/man/pfilter.Rd
pkg/pomp/man/pmcmc.Rd
pkg/pomp/man/pomp-package.Rd
pkg/pomp/man/pomp.Rd
pkg/pomp/man/prior-pomp.Rd
pkg/pomp/man/ricker.Rd
pkg/pomp/man/rw2.Rd
pkg/pomp/man/sannbox.Rd
pkg/pomp/man/simulate-pomp.Rd
Log:
- much editing of the help pages
- remove tutorials and manuals from inst/doc, replace with links to pomp website
- fix bug in 'pompCBuilder'.
Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION 2014-05-13 12:31:28 UTC (rev 949)
+++ pkg/pomp/DESCRIPTION 2014-05-16 16:39:56 UTC (rev 950)
@@ -1,8 +1,8 @@
Package: pomp
Type: Package
Title: Statistical inference for partially observed Markov processes
-Version: 0.50-5
-Date: 2014-05-13
+Version: 0.50-6
+Date: 2014-05-16
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")),
Modified: pkg/pomp/R/builder.R
===================================================================
--- pkg/pomp/R/builder.R 2014-05-13 12:31:28 UTC (rev 949)
+++ pkg/pomp/R/builder.R 2014-05-16 16:39:56 UTC (rev 950)
@@ -133,7 +133,8 @@
parameter.transform="\n}\n\n",
parameter.inv.transform="\n}\n\n",
rprior="\n}\n\n",
- dprior="\n}\n\n"
+ dprior="\n}\n\n",
+ globals="\n"
)
utility.fns <- list()
@@ -192,7 +193,7 @@
cat(file=out,f)
}
- cat(file=out,globals)
+ cat(file=out,globals,footer$globals)
## variable/parameter/observations definitions
for (v in seq_along(paramnames)) {
Modified: pkg/pomp/inst/NEWS
===================================================================
--- pkg/pomp/inst/NEWS 2014-05-13 12:31:28 UTC (rev 949)
+++ pkg/pomp/inst/NEWS 2014-05-16 16:39:56 UTC (rev 950)
@@ -1,5 +1,14 @@
_N_e_w_s _f_o_r _p_a_c_k_a_g_e '_p_o_m_p'
+_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _0._5_0-_6:
+
+ • The package manual and tutorials are no longer included with
+ the package source. Instead, links are provided to the
+ ‘pomp’ website.
+
+ • The package help pages have been revisited for accuracy and
+ completeness.
+
_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _0._5_0-_1:
• ‘pomp’ can now take snippets of C code directly as
Modified: pkg/pomp/inst/NEWS.Rd
===================================================================
--- pkg/pomp/inst/NEWS.Rd 2014-05-13 12:31:28 UTC (rev 949)
+++ pkg/pomp/inst/NEWS.Rd 2014-05-16 16:39:56 UTC (rev 950)
@@ -1,5 +1,12 @@
\name{NEWS}
\title{News for package `pomp'}
+\section{Changes in \pkg{pomp} version 0.50-6}{
+ \itemize{
+ \item The package manual and tutorials are no longer included with the package source.
+ Instead, links are provided to the \pkg{pomp} website.
+ \item The package help pages have been revisited for accuracy and completeness.
+ }
+}
\section{Changes in \pkg{pomp} version 0.50-1}{
\itemize{
\item \code{pomp} can now take snippets of C code directly as definitions of the various basic functions.
Deleted: pkg/pomp/inst/doc/advanced_topics_in_pomp.pdf
===================================================================
(Binary files differ)
Modified: pkg/pomp/inst/doc/index.html
===================================================================
--- pkg/pomp/inst/doc/index.html 2014-05-13 12:31:28 UTC (rev 949)
+++ pkg/pomp/inst/doc/index.html 2014-05-16 16:39:56 UTC (rev 950)
@@ -1,21 +1,29 @@
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
-<title>pomp user guides and other documentation</title>
+<title>pomp user guides and tutorials</title>
<link rel="stylesheet" type="text/css" href="../../R.css">
</head>
<body>
<h2><b>pomp</b> user guides and other documentation</h2>
-<dl>
-<dt><a href="intro_to_pomp.pdf">intro_to_pomp.pdf</a>:</dt>
-<dd>Introduction to <b>pomp</b></dd>
-<dt><a href=
-"advanced_topics_in_pomp.pdf">advanced_topics_in_pomp.pdf</a>:</dt>
-<dd>Advanced topics in <b>pomp</b></dd>
-<dt><a href="manual.pdf">manual.pdf</a>:</dt>
-<dd><b>pomp</b> user manual</dd>
-</dl>
+<table>
+<tr>
+<td>Introduction to <strong>pomp</strong></td>
+<td><a target="_blank" href="http://pomp.r-forge.r-project.org/vignettes/intro_to_pomp.pdf">(PDF)</a></td>
+<td><a target="_blank" href="http://pomp.r-forge.r-project.org/vignettes/intro_to_pomp.R">(R code)</a></td>
+</tr>
+<tr>
+<td>Advanced topics in <strong>pomp</strong></td>
+<td><a target="_blank" href="http://pomp.r-forge.r-project.org/vignettes/advanced_topics_in_pomp.pdf">(PDF)</a></td>
+<td><a target="_blank" href="http://pomp.r-forge.r-project.org/vignettes/advanced_topics_in_pomp.R">(R code)</a></td>
+</tr>
+<tr>
+<td><strong>pomp</strong> package manual</td>
+<td><a target="_blank" href="http://pomp.r-forge.r-project.org/vignettes/pomp.pdf">(PDF)</a></td>
+</tr>
+</table>
+
<p><a href="../html/00Index.html">Back to <b>pomp</b> package index</p>
</body>
</html>
Deleted: pkg/pomp/inst/doc/intro_to_pomp.pdf
===================================================================
(Binary files differ)
Deleted: pkg/pomp/inst/doc/manual.pdf
===================================================================
(Binary files differ)
Modified: pkg/pomp/man/basic-probes.Rd
===================================================================
--- pkg/pomp/man/basic-probes.Rd 2014-05-13 12:31:28 UTC (rev 949)
+++ pkg/pomp/man/basic-probes.Rd 2014-05-16 16:39:56 UTC (rev 950)
@@ -138,8 +138,7 @@
Aaron A. King (kingaa at umich dot edu)
}
\seealso{
- \link{pomp-class},
- \link{pomp-methods}
+ \link{pomp}
}
\keyword{models}
\keyword{ts}
Modified: pkg/pomp/man/blowflies.Rd
===================================================================
--- pkg/pomp/man/blowflies.Rd 2014-05-13 12:31:28 UTC (rev 949)
+++ pkg/pomp/man/blowflies.Rd 2014-05-16 16:39:56 UTC (rev 950)
@@ -37,7 +37,7 @@
to view the code that constructs these pomp objects.
}
-\seealso{\code{\link{pomp-class}} and the vignettes}
+\seealso{\code{\link{pomp}}}
\references{
A. J. Nicholson (1957)
The self-adjustment of populations to change.
Modified: pkg/pomp/man/bsmc.Rd
===================================================================
--- pkg/pomp/man/bsmc.Rd 2014-05-13 12:31:28 UTC (rev 949)
+++ pkg/pomp/man/bsmc.Rd 2014-05-16 16:39:56 UTC (rev 950)
@@ -107,14 +107,21 @@
There are two ways to specify the prior distribution of particles.
If \code{params} is unspecified or is a named vector, \code{Np} draws are made from the prior distribution, as specified by \code{\link{rprior}}.
Alternatively, \code{params} can be specified as an \code{npars} x \code{Np} matrix (with rownames).
- }
+}
\author{
Michael Lavine (lavine at math dot umass dot edu),
Matthew Ferrari (mferrari at psu dot edu),
Aaron A. King
}
+\references{
+ Liu, J. and M. West.
+ Combining Parameter and State Estimation in Simulation-Based Filtering.
+ In A. Doucet, N. de Freitas, and N. J. Gordon, editors,
+ Sequential Monte Carlo Methods in Practice, pages 197-224.
+ Springer, New York, 2001.
+}
\examples{
-## See the vignettes for examples.
+## See the "Introducton to pomp" document for examples.
}
\seealso{\link{pomp-class}}
\keyword{ts}
Modified: pkg/pomp/man/builder.Rd
===================================================================
--- pkg/pomp/man/builder.Rd 2014-05-13 12:31:28 UTC (rev 949)
+++ pkg/pomp/man/builder.Rd 2014-05-16 16:39:56 UTC (rev 950)
@@ -2,7 +2,7 @@
\alias{pompBuilder}
\title{Write, compile, link, and build a pomp object using native codes}
\description{
- \code{pompBuilder} is an EXPERIMENTAL facility for producing compiled \code{pomp} objects.
+ \code{pompBuilder} is a facility for producing compiled \code{pomp} objects.
}
\usage{
pompBuilder(data, times, t0, name, statenames, paramnames,
Modified: pkg/pomp/man/mif-methods.Rd
===================================================================
--- pkg/pomp/man/mif-methods.Rd 2014-05-13 12:31:28 UTC (rev 949)
+++ pkg/pomp/man/mif-methods.Rd 2014-05-16 16:39:56 UTC (rev 950)
@@ -51,6 +51,6 @@
}
}
\author{Aaron A. King \email{kingaa at umich dot edu}}
-\seealso{\code{\link{mif}}, \code{\link{pomp}}, \code{\link{pomp-class}}, \code{\link{pfilter}}}
+\seealso{\code{\link{mif}}, \code{\link{pomp}}, \code{\link{pfilter}}}
\keyword{models}
\keyword{ts}
Modified: pkg/pomp/man/mif.Rd
===================================================================
--- pkg/pomp/man/mif.Rd 2014-05-13 12:31:28 UTC (rev 949)
+++ pkg/pomp/man/mif.Rd 2014-05-16 16:39:56 UTC (rev 950)
@@ -11,9 +11,9 @@
\alias{continue,mif-method}
\alias{continue-mif}
\alias{mif-class}
-\title{The MIF algorithm}
+\title{Iterated filtering}
\description{
- The MIF algorithm for estimating the parameters of a partially-observed Markov process.
+ Iterated filtering algorithms for estimating the parameters of a partially-observed Markov process.
}
\usage{
mif(object, \dots)
@@ -35,7 +35,7 @@
An object of class \code{pomp}.
}
\item{Nmif}{
- The number of MIF iterations to perform.
+ The number of filtering iterations to perform.
}
\item{start}{
named numerical vector;
@@ -82,7 +82,7 @@
The \code{mif} update for initial-value parameters consists of replacing them by their filtering mean at time \code{times[ic.lag]}, where \code{times=time(object)}.
It makes no sense to set \code{ic.lag>length(times)};
if it is so set, \code{ic.lag} is set to \code{length(times)} with a warning.
- For \code{method='mif2'}, the default is \code{ic.lag=length(times)}.
+ For \code{method="mif2"}, the default is \code{ic.lag=length(times)}.
}
\item{var.factor}{
a positive number;
@@ -103,7 +103,7 @@
\code{method="mif"} uses the iterated filtering update rule (Ionides 2006, 2011);
\code{method="unweighted"} updates the parameter to the unweighted average of the filtering means of the parameters at each time;
\code{method="fp"} updates the parameter to the filtering mean at the end of the time series.
- \code{method="mif2"} [EXPLAIN]
+% \code{method="mif2"}
}
\item{tol}{
See the description under \code{\link{pfilter}}.
@@ -149,7 +149,7 @@
\code{Np} may be assumed to be a positive integer;
\code{center} and \code{sd} will be named vectors of the same length.
Additional arguments may be specified;
- these will be filled with the elements of the \code{userdata} slot of the underlying \code{pomp} object (see \code{\link{pomp-class}}).
+ these will be filled with the elements of the \code{userdata} slot of the underlying \code{pomp} object (see \code{\link{pomp}}).
\code{particles} returns a \code{length(center)} x \code{Np} matrix with rownames matching the names of \code{center} and \code{sd}.
Each column represents a distinct particle.
@@ -173,7 +173,7 @@
}
\author{Aaron A. King \email{kingaa at umich dot edu}}
\seealso{
- \code{\link{mif-methods}}, \code{\link{pomp}}, \code{\link{pomp-class}}, \code{\link{pfilter}}.
+ \code{\link{mif-methods}}, \code{\link{pomp}}, \code{\link{pfilter}}.
See the \dQuote{intro_to_pomp} vignette for examples.
}
\keyword{ts}
Modified: pkg/pomp/man/nlf.Rd
===================================================================
--- pkg/pomp/man/nlf.Rd 2014-05-13 12:31:28 UTC (rev 949)
+++ pkg/pomp/man/nlf.Rd 2014-05-16 16:39:56 UTC (rev 950)
@@ -110,12 +110,10 @@
Kendall, B. E., Briggs, C. J., Murdoch, W. W., Turchin, P., Ellner, S. P., McCauley, E., Nisbet, R. M. and Wood S. N. (1999)
Why do populations cycle? A synthesis of statistical and mechanistic modeling approaches.
\emph{Ecology} \bold{80}, 1789--1805.
- Available online at \url{http://www2.bren.ucsb.edu/~kendall/pubs/1999Ecology.pdf}
Kendall, B. E., Ellner, S. P., McCauley, E., Wood, S. N., Briggs, C. J., Murdoch, W. W. and Turchin, P. (2005)
Population cycles in the pine looper moth (\emph{Bupalus piniarius}): dynamical tests of mechanistic hypotheses.
\emph{Ecological Monographs} \bold{75}, 259--276.
- Available online at \url{http://repositories.cdlib.org/postprints/818/}
}
\author{Stephen P. Ellner \email{spe2 at cornell dot edu} and Bruce E. Kendall \email{kendall at bren dot ucsb dot edu}}
\keyword{models}
Modified: pkg/pomp/man/pfilter.Rd
===================================================================
--- pkg/pomp/man/pfilter.Rd 2014-05-13 12:31:28 UTC (rev 949)
+++ pkg/pomp/man/pfilter.Rd 2014-05-16 16:39:56 UTC (rev 950)
@@ -133,6 +133,6 @@
IEEE Trans. Sig. Proc. 50:174--188, 2002.
}
\author{Aaron A. King \email{kingaa at umich dot edu}}
-\seealso{\link{pomp-class}}
+\seealso{\code{\link{pomp}}, \code{\link{mif}}, \code{\link{pmcmc}}, \code{\link{bsmc}}}
\keyword{models}
\keyword{ts}
Modified: pkg/pomp/man/pmcmc.Rd
===================================================================
--- pkg/pomp/man/pmcmc.Rd 2014-05-13 12:31:28 UTC (rev 949)
+++ pkg/pomp/man/pmcmc.Rd 2014-05-16 16:39:56 UTC (rev 950)
@@ -73,18 +73,6 @@
}
\value{
An object of class \code{pmcmc}.
- This class inherits from class \code{\link[=pfilterd.pomp-class]{pfilterd.pomp}} and contains the following additional slots:
- \describe{
- \item{pars, Nmcmc, dprior, hyperparams}{
- These slots hold the values of the corresponding arguments of the call to \code{pmcmc}.
- }
- \item{random.walk.sd}{
- a named numeric vector containing the random-walk variances used to parameterize a Gaussian random walk MCMC proposal.
- }
- \item{log.prior}{
- a numeric value containing the log of the prior density evaluated at the parameter vector in the params slot.
- }
- }
}
\section{Re-running PMCMC Iterations}{
To re-run a sequence of PMCMC iterations, one can use the \code{pmcmc} method on a \code{pmcmc} object.
@@ -100,7 +88,7 @@
\section{Details}{
\code{pmcmc} implements an MCMC algorithm in which the true likelihood of the data is replaced by an unbiased estimate computed by a particle filter.
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 (Andrieu et al, 2010) has not yet been implemented.
+ An extension to give a correct Bayesian posterior distribution of unobserved state variables (as in Andrieu et al, 2010) has not yet been implemented.
}
\references{
C. Andrieu, A. Doucet and R. Holenstein,
Modified: pkg/pomp/man/pomp-package.Rd
===================================================================
--- pkg/pomp/man/pomp-package.Rd 2014-05-13 12:31:28 UTC (rev 949)
+++ pkg/pomp/man/pomp-package.Rd 2014-05-16 16:39:56 UTC (rev 950)
@@ -3,43 +3,47 @@
\alias{pomp-package}
\title{Partially-observed Markov processes}
\description{
-%% This is documentation for version \Sexpr[echo=F,stage=install,results=text]{packageDescription("pomp",fields="Version")} of \pkg{pomp}.
-
The \pkg{pomp} package provides facilities for inference on time series data using partially-observed Markov processes (AKA state-space models or nonlinear stochastic dynamical systems).
One can use \pkg{pomp} to fit nonlinear, non-Gaussian dynamic models to time-series data.
The first step in using \pkg{pomp} is to encode one's model and data in an object of class \code{pomp}.
One does this via a call to \code{\link{pomp}}, which involves specifying the process and measurement components of the model in one or more of a variety of ways.
- Details on this are given in the documentation for the \code{\link{pomp}} function and examples are given in the \sQuote{intro_to_pomp} vignette.
+ Details on this are given in the documentation for the \code{\link{pomp}} function.
+ Examples are given in the \sQuote{Introduction to \pkg{pomp}} document, in the demos (\code{demo(package='pomp')}), and via the \code{\link{pompExample}} function.
- Currently, \pkg{pomp} provides algorithms for
- (i) simulation of stochastic dynamical systems (see \code{\link[=simulate-pomp]{simulate}}),
- (ii) particle filtering (AKA sequential Monte Carlo or sequential importance sampling), see \code{\link{pfilter}}),
- (iii) the iterated filtering method of Ionides et al. (2006), see \code{\link{mif}}),
- (iv) the nonlinear forecasting algorithm of Kendall et al. (2005), see \code{\link{nlf}}),
- (v) the particle MCMC approach of Andrieu et al. (2010), see \code{\link{pmcmc}},
- (vi) basic trajectory matching, see \code{\link{traj.match}},
- (vi) the probe-matching method of Wood (2010) and Kendall et al. (1999), see \code{\link{probe.match}},
- (vii) a spectral probe-matching method (Reuman et al., 2006), see \code{\link{spect.match}}.
- See the package website \url{http://pomp.r-forge.r-project.org} for these references.
+ \pkg{pomp} version \Sexpr[echo=F,stage=install,results=text]{packageDescription("pomp",fields="Version")} provides algorithms for
+ \enumerate{
+ \item simulation of stochastic dynamical systems; see \code{\link[=simulate-pomp]{simulate}}
+ \item particle filtering (AKA sequential Monte Carlo or sequential importance sampling); see \code{\link{pfilter}}
+ \item the iterated filtering method of Ionides et al. (2006, 2011); see \code{\link{mif}}
+ \item the nonlinear forecasting algorithm of Kendall et al. (2005); see \code{\link{nlf}}
+ \item the particle MCMC approach of Andrieu et al. (2010); see \code{\link{pmcmc}}
+ \item the probe-matching method of Kendall et al. (1999, 2005); see \code{\link{probe.match}}
+ \item a spectral probe-matching method (Reuman et al. 2006, 2008); see \code{\link{spect.match}}
+ \item synthetic likelihood a la Wood (2010); see \code{\link{probe}}
+ \item approximate Bayesian computation (Toni et al. 2009); see \code{\link{abc}}
+ \item the approximate Bayesian sequential Monte Carlo scheme of Liu & West (2001); see \code{\link{bsmc}}
+ \item basic trajectory matching; see \code{\link{traj.match}}.
+ }
The package also provides various tools for plotting and extracting information on models and data as well as an API for algorithm development.
- Future support for additional algorithms in envisioned, and implementations of
- the Bayesian sequential Monte Carlo approach of Liu \& West.
- Much of the work in \pkg{pomp} has been done under the auspices of a working group of the National Center for Ecological Analysis and Synthesis (\acronym{NCEAS}), "Inference for Mechanistic Models".
+ Future support for additional algorithms in envisioned.
+ Much of the groundwork for \pkg{pomp} was laid by a working group of the National Center for Ecological Analysis and Synthesis (\acronym{NCEAS}), \dQuote{Inference for Mechanistic Models}.
- The package is provided under the \acronym{GNU} Public License (\acronym{GPL}).
- Contributions are welcome, as are comments, suggestions for improvements, and bug reports.
- See the package website \url{http://pomp.r-forge.r-project.org} for more information, access to the package mailing list, links to the authors' websites, and references to the literature.
+ \pkg{pomp} is provided under the \acronym{GNU} Public License (\acronym{GPL}).
+ Contributions are welcome, as are comments, feature requests, and bug reports.
+ See the package website \url{http://pomp.r-forge.r-project.org} for more information, access to the package mailing list, links to the authors' websites, references to the literature, and up-to-date versions of the package source and documentation.
}
\section{Classes}{
\pkg{pomp} makes extensive use of S4 classes.
The basic class, \code{\link{pomp}}, encodes a partially-observed Markov process together with a uni- or multi-variate data set and (possibly) parameters.
}
-\section{Vignettes}{
- The vignette \sQuote{Introduction to pomp} illustrates the facilities of the package using familiar stochastic processes.
- Methods for accelerating your codes are discussed in the \sQuote{Advanced topics in pomp} vignette.
- These vignettes are installed in the package \code{doc} directory and are accessible via the HTML documentation.
- They can also be viewed at \url{http://pomp.r-forge.r-project.org}.
+\section{Documentation}{
+ The \href{http://pomp.r-forge.r-project.org/vignettes/index.html}{\sQuote{Introduction to \pkg{pomp}}} document illustrates the facilities of the package using familiar stochastic processes.
+ The \href{http://pomp.r-forge.r-project.org/vignettes/index.html}{\sQuote{Advanced topics in \pkg{pomp}}} document discusses the low-level interface and some more advanced modeling techniques.
+ These documents can be viewed at \url{http://pomp.r-forge.r-project.org}.
}
+\references{
+ See the package website, \url{http://pomp.r-forge.r-project.org}, for the references.
+}
\author{Aaron A. King \email{kingaa at umich dot edu}}
\seealso{
\code{\link{pomp}},
Modified: pkg/pomp/man/pomp.Rd
===================================================================
--- pkg/pomp/man/pomp.Rd 2014-05-13 12:31:28 UTC (rev 949)
+++ pkg/pomp/man/pomp.Rd 2014-05-16 16:39:56 UTC (rev 950)
@@ -91,7 +91,6 @@
optional; a formula or list of formulae, specifying the measurement model.
These formulae are parsed internally to generate \code{rmeasure} and \code{dmeasure} functions.
If \code{measurement.model} is given it overrides any specification of \code{rmeasure} or \code{dmeasure}.
- See below for an example.
\strong{NB:} This is a convenience function, primarily designed to facilitate exploration;
it will typically be possible to acclerate measurement model computations by writing \code{dmeasure} and/or \code{rmeasure} functions directly.
}
@@ -103,8 +102,8 @@
indicate this by specifying \code{skeleton.type="vectorfield"}.
The skeleton function can be specified in one of three ways:
- (1) as an \R function of prototype \preformatted{skeleton(x,t,params,\dots)} that evaluates the deterministic skeleton at state \code{x} and time \code{t} given the parameters \code{params}, or
- (2) as a snippet of C code (via \code{\link{Csnippet}}) that performs this evaluation.
+ (1) as an \R function of prototype \preformatted{skeleton(x,t,params,\dots)} that evaluates the deterministic skeleton at state \code{x} and time \code{t} given the parameters \code{params},
+ (2) as a snippet of C code (via \code{\link{Csnippet}}) that performs this evaluation, or
(3) as the name of a native (compiled) routine with prototype \dQuote{pomp_skeleton} as defined in the header file \dQuote{pomp.h}.
If the deterministic skeleton depends on covariates, the optional argument \code{covars} will be filled with interpolated values of the covariates at the time \code{t}.
@@ -122,7 +121,7 @@
optional; function drawing a sample from a prior distribution on parameters.
This can be specified in one of three ways:
(1) as an \R function of prototype \preformatted{rprior(params,\dots)} that makes a draw from the prior distribution given \code{params},
- (2) as a snippet of C code (via \code{\link{Csnippet}}) that draws from the prior,
+ (2) as a snippet of C code (via \code{\link{Csnippet}}) that draws from the prior, or
(3) as the name of a native (compiled) routine with prototype \dQuote{pomp_rprior} as defined in the header file \dQuote{pomp.h}.
}
\item{dprior}{
@@ -301,8 +300,9 @@
}
}
\examples{
-## For examples, see the vignettes, the data()-loadable
-## example \code{pomp} objects, and the provided example files.
+## For examples, see the \dQuote{Introduction to \pkg{pomp}}
+## and \dQuote{Advanced topics in \pkg{pomp}} documents,
+## the demos, and the examples provided with the package, e.g.:
\dontrun{
pompExample()
pomp.home <- system.file("examples",package="pomp")
Modified: pkg/pomp/man/prior-pomp.Rd
===================================================================
--- pkg/pomp/man/prior-pomp.Rd 2014-05-13 12:31:28 UTC (rev 949)
+++ pkg/pomp/man/prior-pomp.Rd 2014-05-16 16:39:56 UTC (rev 950)
@@ -30,6 +30,6 @@
For specifications on writing these functions, see \code{\link{pomp}}.
}
\author{Aaron A. King \email{kingaa at umich dot edu}}
-\seealso{\code{\link{pomp-class}}, \code{\link{pomp}}}
+\seealso{\code{\link{pomp}}}
\keyword{models}
\keyword{ts}
Modified: pkg/pomp/man/ricker.Rd
===================================================================
--- pkg/pomp/man/ricker.Rd 2014-05-13 12:31:28 UTC (rev 949)
+++ pkg/pomp/man/ricker.Rd 2014-05-16 16:39:56 UTC (rev 950)
@@ -14,5 +14,5 @@
plot(ricker)
coef(ricker)
}
-\seealso{\code{\link{pomp-class}} and the vignettes}
+\seealso{\code{\link{pomp}} and the vignettes}
\keyword{datasets}
Modified: pkg/pomp/man/rw2.Rd
===================================================================
--- pkg/pomp/man/rw2.Rd 2014-05-13 12:31:28 UTC (rev 949)
+++ pkg/pomp/man/rw2.Rd 2014-05-16 16:39:56 UTC (rev 950)
@@ -14,5 +14,5 @@
x <- simulate(rw2,nsim=10,seed=20348585L,params=c(x1.0=0,x2.0=0,s1=1,s2=3,tau=1))
plot(x[[1]])
}
-\seealso{\code{\link{pomp-class}} and the vignettes}
+\seealso{\code{\link{pomp}} and the vignettes}
\keyword{datasets}
Modified: pkg/pomp/man/sannbox.Rd
===================================================================
--- pkg/pomp/man/sannbox.Rd 2014-05-13 12:31:28 UTC (rev 949)
+++ pkg/pomp/man/sannbox.Rd 2014-05-16 16:39:56 UTC (rev 950)
@@ -52,12 +52,12 @@
\item{\code{candidate.dist}}{
function to randomly select a new candidate parameter vector.
This should be a function with three arguments, the first being the current parameter vector, the second the temperature, and the third the parameter scaling.
- By default, \code{candidate.dist} is \code{function(par,temp,scale) rnorm(n=length(par),mean=par,sd=scale*temp)}.
+ By default, \code{candidate.dist} is \preformatted{function(par,temp,scale) rnorm(n=length(par),mean=par,sd=scale*temp)}.
}
\item{\code{sched}}{
cooling schedule.
A function of a three arguments giving the temperature as a function of iteration number and the control parameters \code{temp} and \code{tmax}.
- By default, \code{sched} is \code{function(k,temp,tmax) temp/log(((k-1)\%/\%tmax)*tmax+exp(1))}.
+ By default, \code{sched} is \preformatted{function(k,temp,tmax) temp/log(((k-1)\%/\%tmax)*tmax+exp(1))}.
Alternatively, one can supply a numeric vector of temperatures.
This must be of length at least \code{maxit}.
Modified: pkg/pomp/man/simulate-pomp.Rd
===================================================================
--- pkg/pomp/man/simulate-pomp.Rd 2014-05-13 12:31:28 UTC (rev 949)
+++ pkg/pomp/man/simulate-pomp.Rd 2014-05-16 16:39:56 UTC (rev 950)
@@ -66,6 +66,6 @@
x <- simulate(ou2,seed=3495485,nsim=10,states=TRUE,obs=TRUE)
}
\author{Aaron A. King \email{kingaa at umich dot edu}}
-\seealso{\link{pomp-class}}
+\seealso{\link{pomp}}
\keyword{models}
\keyword{ts}
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