[Pomp-commits] r1131 - pkg pkg/pomp/man www www/content www/help www/vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Mar 4 14:09:19 CET 2015
Author: kingaa
Date: 2015-03-04 14:09:19 +0100 (Wed, 04 Mar 2015)
New Revision: 1131
Added:
www/help/
www/help/00Index.html
www/help/00frame_toc.html
www/help/LondonYorke.html
www/help/Makefile
www/help/R.css
www/help/abc.html
www/help/basic-probes.html
www/help/blowflies.html
www/help/bsmc.html
www/help/bsplines.html
www/help/builder.html
www/help/csnippet.html
www/help/dacca.html
www/help/design.html
www/help/eulermultinom.html
www/help/example.html
www/help/gompertz.html
www/help/index.html
www/help/logmeanexp.html
www/help/lowlevel.html
www/help/mif.html
www/help/nlf.html
www/help/ou2.html
www/help/parmat.html
www/help/particles-mif.html
www/help/pfilter.html
www/help/plugins.html
www/help/pmcmc.html
www/help/pomp-fun.html
www/help/pomp-methods.html
www/help/pomp-package.html
www/help/pomp.html
www/help/pomp.pdf
www/help/probe.html
www/help/proposals.html
www/help/ricker.html
www/help/rw2.html
www/help/sannbox.html
www/help/simulate-pomp.html
www/help/sir.html
www/help/spect.html
www/help/traj-match.html
Removed:
www/vignettes/index.html
www/vignettes/pomp.pdf
Modified:
pkg/Makefile
pkg/pomp/man/example.Rd
www/content/vignettes.htm
www/index.php
www/vignettes/Makefile
Log:
- add html version of manual to package website
Modified: pkg/Makefile
===================================================================
--- pkg/Makefile 2015-03-04 13:09:14 UTC (rev 1130)
+++ pkg/Makefile 2015-03-04 13:09:19 UTC (rev 1131)
@@ -32,12 +32,12 @@
%.dist %.manual %.vignettes: export R_QPDF=qpdf
%.dist %.manual %.vignettes: export R_GSCMD=gs
%.dist %.manual %.vignettes: export GS_QUALITY=ebook
-%.dist %.manual %.vignettes: export R_HOME=$(shell $(REXE) RHOME)
+%.dist %.manual %.vignettes %.help: export R_HOME=$(shell $(REXE) RHOME)
%.check %.crancheck: export _R_CHECK_ALL_NON_ISO_C_=TRUE
%.crancheck: export R_PROFILE_USER=./Rprofile
%.check %.crancheck: export _R_CHECK_WALL_FORTRAN_=TRUE
%.check %.xcheck: export POMP_FULL_TESTS=yes
-%.vignettes %.data: export R_LIBS=$(CURDIR)/library
+%.vignettes %.help %.data: export R_LIBS=$(CURDIR)/library
%.bin %.check %.qcheck %.qqcheck %.xcheck %.crancheck %.upload %.publish %.clean %.install %.win: PKG = $*_$(shell perl -ne 'print $$1 if /Version:\s+(\d+\.\d+-\d+)/;' $*/DESCRIPTION)
pomp.vignettes: pomp.install pomp.manual
@@ -48,6 +48,9 @@
pompExamples.vignettes: pompExamples.install
(cd pompExamples/vignettes; make)
+pomp.help: pomp.install
+ (cd ../www/help; make)
+
%.data: %.install
cd $*/inst/data-R; make
Modified: pkg/pomp/man/example.Rd
===================================================================
--- pkg/pomp/man/example.Rd 2015-03-04 13:09:14 UTC (rev 1130)
+++ pkg/pomp/man/example.Rd 2015-03-04 13:09:19 UTC (rev 1131)
@@ -40,8 +40,10 @@
pompExample(euler.sir)
pompExample("gompertz")
pompExample(ricker,envir=NULL)
+\dontrun{
file.show(system.file("examples/bbs.R",package="pomp"))
}
+}
\seealso{
\code{\link{blowflies}}, \code{\link{dacca}}, \code{\link{gompertz}},
\code{\link{ou2}}, \code{\link{ricker}}, \code{\link{rw2}},
Modified: www/content/vignettes.htm
===================================================================
--- www/content/vignettes.htm 2015-03-04 13:09:14 UTC (rev 1130)
+++ www/content/vignettes.htm 2015-03-04 13:09:19 UTC (rev 1131)
@@ -7,6 +7,7 @@
<td><a target="_blank" href="vignettes/getting_started.R">(R code)</a></td>
</tr>
<td><strong>pomp</strong> package manual</td>
-<td><a target="_blank" href="vignettes/pomp.pdf">(PDF)</a></td>
+<td><a target="_blank" href="help/pomp-package.html">(HTML)</a></td>
+<td><a target="_blank" href="help/pomp.pdf">(PDF)</a></td>
</tr>
</table>
Added: www/help/00Index.html
===================================================================
--- www/help/00Index.html (rev 0)
+++ www/help/00Index.html 2015-03-04 13:09:19 UTC (rev 1131)
@@ -0,0 +1,810 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head><title>R: Statistical Inference for Partially Observed Markov Processes</title>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" type="text/css" href="R.css">
+</head><body>
+<h1> Statistical Inference for Partially Observed Markov Processes
+<img class="toplogo" src="http://stat.ethz.ch/R-manual/R-devel/doc/html/logo.jpg" alt="[R logo]">
+</h1>
+<hr>
+<div align="center">
+<a href="http://stat.ethz.ch/R-manual/R-devel/doc/html/packages.html"><img src="http://stat.ethz.ch/R-manual/R-devel/doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
+<a href="http://stat.ethz.ch/R-manual/R-devel/doc/html/index.html"><img src="http://stat.ethz.ch/R-manual/R-devel/doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
+</div><h2>Documentation for package ‘pomp’ version 0.62-5</h2>
+
+<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
+<li><a href="../doc/index.html">User guides, package vignettes and other documentation.</a></li>
+<li><a href="../demo">Code demos</a>. Use <a href="../../utils/help/demo">demo()</a> to run them.</li>
+<li><a href="../NEWS">Package NEWS</a>.</li>
+</ul>
+
+<h2>Help Pages</h2>
+
+
+<p align="center">
+<a href="# "> </a>
+<a href="#A">A</a>
+<a href="#B">B</a>
+<a href="#C">C</a>
+<a href="#D">D</a>
+<a href="#E">E</a>
+<a href="#F">F</a>
+<a href="#G">G</a>
+<a href="#I">I</a>
+<a href="#L">L</a>
+<a href="#M">M</a>
+<a href="#N">N</a>
+<a href="#O">O</a>
+<a href="#P">P</a>
+<a href="#R">R</a>
+<a href="#S">S</a>
+<a href="#T">T</a>
+<a href="#V">V</a>
+<a href="#W">W</a>
+<a href="#misc">misc</a>
+</p>
+
+<table width="100%">
+<tr><td width="25%"><a href="pomp-package.html">pomp-package</a></td>
+<td>Inference for partially observed Markov processes</td></tr>
+</table>
+
+<h2><a name="A">-- A --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="abc.html">ABC</a></td>
+<td>Estimation by approximate Bayesian computation (ABC)</td></tr>
+<tr><td width="25%"><a href="abc.html">abc</a></td>
+<td>Estimation by approximate Bayesian computation (ABC)</td></tr>
+<tr><td width="25%"><a href="abc.html">abc-abc</a></td>
+<td>Estimation by approximate Bayesian computation (ABC)</td></tr>
+<tr><td width="25%"><a href="abc.html">abc-class</a></td>
+<td>Estimation by approximate Bayesian computation (ABC)</td></tr>
+<tr><td width="25%"><a href="abc.html">abc-method</a></td>
+<td>Estimation by approximate Bayesian computation (ABC)</td></tr>
+<tr><td width="25%"><a href="abc.html">abc-methods</a></td>
+<td>Estimation by approximate Bayesian computation (ABC)</td></tr>
+<tr><td width="25%"><a href="abc.html">abc-pomp</a></td>
+<td>Estimation by approximate Bayesian computation (ABC)</td></tr>
+<tr><td width="25%"><a href="abc.html">abc-probed.pomp</a></td>
+<td>Estimation by approximate Bayesian computation (ABC)</td></tr>
+<tr><td width="25%"><a href="abc.html">abcList-class</a></td>
+<td>Estimation by approximate Bayesian computation (ABC)</td></tr>
+<tr><td width="25%"><a href="pomp.html">accumulator variables</a></td>
+<td>Constructor of the basic POMP object</td></tr>
+<tr><td width="25%"><a href="pfilter.html">as-method</a></td>
+<td>Particle filter</td></tr>
+<tr><td width="25%"><a href="pomp-methods.html">as-method</a></td>
+<td>Functions for manipulating, displaying, and extracting information from objects of the 'pomp' class</td></tr>
+<tr><td width="25%"><a href="probe.html">as-method</a></td>
+<td>Probe a partially-observed Markov process by computing summary statistics and the synthetic likelihood.</td></tr>
+<tr><td width="25%"><a href="pfilter.html">as.data.frame.pfilterd.pomp</a></td>
+<td>Particle filter</td></tr>
+<tr><td width="25%"><a href="pomp-methods.html">as.data.frame.pomp</a></td>
+<td>Functions for manipulating, displaying, and extracting information from objects of the 'pomp' class</td></tr>
+</table>
+
+<h2><a name="B">-- B --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="basic-probes.html">basic.probes</a></td>
+<td>Some useful probes for partially-observed Markov processes</td></tr>
+<tr><td width="25%"><a href="bsmc.html">Bayesian sequential Monte Carlo</a></td>
+<td>The Liu and West Bayesian particle filter</td></tr>
+<tr><td width="25%"><a href="sir.html">bbs</a></td>
+<td>Compartmental epidemiological models</td></tr>
+<tr><td width="25%"><a href="blowflies.html">blowflies</a></td>
+<td>Model for Nicholson's blowflies.</td></tr>
+<tr><td width="25%"><a href="blowflies.html">blowflies1</a></td>
+<td>Model for Nicholson's blowflies.</td></tr>
+<tr><td width="25%"><a href="blowflies.html">blowflies2</a></td>
+<td>Model for Nicholson's blowflies.</td></tr>
+<tr><td width="25%"><a href="bsmc.html">bsmc</a></td>
+<td>The Liu and West Bayesian particle filter</td></tr>
+<tr><td width="25%"><a href="bsmc.html">bsmc-method</a></td>
+<td>The Liu and West Bayesian particle filter</td></tr>
+<tr><td width="25%"><a href="bsmc.html">bsmc-pomp</a></td>
+<td>The Liu and West Bayesian particle filter</td></tr>
+<tr><td width="25%"><a href="bsmc.html">bsmc2</a></td>
+<td>The Liu and West Bayesian particle filter</td></tr>
+<tr><td width="25%"><a href="bsmc.html">bsmc2-method</a></td>
+<td>The Liu and West Bayesian particle filter</td></tr>
+<tr><td width="25%"><a href="bsmc.html">bsmc2-pomp</a></td>
+<td>The Liu and West Bayesian particle filter</td></tr>
+<tr><td width="25%"><a href="bsplines.html">bspline.basis</a></td>
+<td>B-spline bases</td></tr>
+</table>
+
+<h2><a name="C">-- C --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="abc.html">c-abc</a></td>
+<td>Estimation by approximate Bayesian computation (ABC)</td></tr>
+<tr><td width="25%"><a href="abc.html">c-abcList</a></td>
+<td>Estimation by approximate Bayesian computation (ABC)</td></tr>
+<tr><td width="25%"><a href="abc.html">c-method</a></td>
+<td>Estimation by approximate Bayesian computation (ABC)</td></tr>
+<tr><td width="25%"><a href="mif.html">c-method</a></td>
+<td>Maximum likelihood by iterated filtering</td></tr>
+<tr><td width="25%"><a href="pmcmc.html">c-method</a></td>
+<td>The particle Markov chain Metropolis-Hastings algorithm</td></tr>
+<tr><td width="25%"><a href="mif.html">c-mif</a></td>
+<td>Maximum likelihood by iterated filtering</td></tr>
+<tr><td width="25%"><a href="mif.html">c-mifList</a></td>
+<td>Maximum likelihood by iterated filtering</td></tr>
+<tr><td width="25%"><a href="pmcmc.html">c-pmcmc</a></td>
+<td>The particle Markov chain Metropolis-Hastings algorithm</td></tr>
+<tr><td width="25%"><a href="pmcmc.html">c-pmcmcList</a></td>
+<td>The particle Markov chain Metropolis-Hastings algorithm</td></tr>
+<tr><td width="25%"><a href="pomp-methods.html">coef-method</a></td>
+<td>Functions for manipulating, displaying, and extracting information from objects of the 'pomp' class</td></tr>
+<tr><td width="25%"><a href="pomp-methods.html">coef-pomp</a></td>
+<td>Functions for manipulating, displaying, and extracting information from objects of the 'pomp' class</td></tr>
+<tr><td width="25%"><a href="pomp-methods.html">coef<-</a></td>
+<td>Functions for manipulating, displaying, and extracting information from objects of the 'pomp' class</td></tr>
+<tr><td width="25%"><a href="pomp-methods.html">coef<--method</a></td>
+<td>Functions for manipulating, displaying, and extracting information from objects of the 'pomp' class</td></tr>
+<tr><td width="25%"><a href="pomp-methods.html">coef<--pomp</a></td>
+<td>Functions for manipulating, displaying, and extracting information from objects of the 'pomp' class</td></tr>
+<tr><td width="25%"><a href="pfilter.html">coerce-method</a></td>
+<td>Particle filter</td></tr>
+<tr><td width="25%"><a href="pomp-methods.html">coerce-method</a></td>
+<td>Functions for manipulating, displaying, and extracting information from objects of the 'pomp' class</td></tr>
+<tr><td width="25%"><a href="probe.html">coerce-method</a></td>
+<td>Probe a partially-observed Markov process by computing summary statistics and the synthetic likelihood.</td></tr>
+<tr><td width="25%"><a href="mif.html">compare.mif</a></td>
+<td>Maximum likelihood by iterated filtering</td></tr>
+<tr><td width="25%"><a href="pfilter.html">cond.logLik</a></td>
+<td>Particle filter</td></tr>
+<tr><td width="25%"><a href="pfilter.html">cond.logLik-method</a></td>
+<td>Particle filter</td></tr>
+<tr><td width="25%"><a href="pfilter.html">cond.logLik-pfilterd.pomp</a></td>
+<td>Particle filter</td></tr>
+<tr><td width="25%"><a href="mif.html">continue</a></td>
+<td>Maximum likelihood by iterated filtering</td></tr>
+<tr><td width="25%"><a href="abc.html">continue-abc</a></td>
+<td>Estimation by approximate Bayesian computation (ABC)</td></tr>
+<tr><td width="25%"><a href="abc.html">continue-method</a></td>
+<td>Estimation by approximate Bayesian computation (ABC)</td></tr>
+<tr><td width="25%"><a href="mif.html">continue-method</a></td>
+<td>Maximum likelihood by iterated filtering</td></tr>
+<tr><td width="25%"><a href="pmcmc.html">continue-method</a></td>
+<td>The particle Markov chain Metropolis-Hastings algorithm</td></tr>
+<tr><td width="25%"><a href="mif.html">continue-mif</a></td>
+<td>Maximum likelihood by iterated filtering</td></tr>
+<tr><td width="25%"><a href="pmcmc.html">continue-pmcmc</a></td>
+<td>The particle Markov chain Metropolis-Hastings algorithm</td></tr>
+<tr><td width="25%"><a href="mif.html">conv.rec</a></td>
+<td>Maximum likelihood by iterated filtering</td></tr>
+<tr><td width="25%"><a href="abc.html">conv.rec-abc</a></td>
+<td>Estimation by approximate Bayesian computation (ABC)</td></tr>
+<tr><td width="25%"><a href="abc.html">conv.rec-abcList</a></td>
+<td>Estimation by approximate Bayesian computation (ABC)</td></tr>
+<tr><td width="25%"><a href="abc.html">conv.rec-method</a></td>
+<td>Estimation by approximate Bayesian computation (ABC)</td></tr>
+<tr><td width="25%"><a href="mif.html">conv.rec-method</a></td>
+<td>Maximum likelihood by iterated filtering</td></tr>
+<tr><td width="25%"><a href="pmcmc.html">conv.rec-method</a></td>
+<td>The particle Markov chain Metropolis-Hastings algorithm</td></tr>
+<tr><td width="25%"><a href="mif.html">conv.rec-mif</a></td>
+<td>Maximum likelihood by iterated filtering</td></tr>
+<tr><td width="25%"><a href="mif.html">conv.rec-mifList</a></td>
+<td>Maximum likelihood by iterated filtering</td></tr>
+<tr><td width="25%"><a href="pmcmc.html">conv.rec-pmcmc</a></td>
+<td>The particle Markov chain Metropolis-Hastings algorithm</td></tr>
+<tr><td width="25%"><a href="pmcmc.html">conv.rec-pmcmcList</a></td>
+<td>The particle Markov chain Metropolis-Hastings algorithm</td></tr>
+<tr><td width="25%"><a href="csnippet.html">Csnippet</a></td>
+<td>C code snippets for accelerating computations</td></tr>
+<tr><td width="25%"><a href="csnippet.html">Csnippet-class</a></td>
+<td>C code snippets for accelerating computations</td></tr>
+</table>
+
+<h2><a name="D">-- D --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="dacca.html">dacca</a></td>
+<td>Model of cholera transmission for historic Bengal.</td></tr>
+<tr><td width="25%"><a href="pomp-methods.html">data.array</a></td>
+<td>Functions for manipulating, displaying, and extracting information from objects of the 'pomp' class</td></tr>
+<tr><td width="25%"><a href="pomp-methods.html">data.array-method</a></td>
+<td>Functions for manipulating, displaying, and extracting information from objects of the 'pomp' class</td></tr>
+<tr><td width="25%"><a href="pomp-methods.html">data.array-pomp</a></td>
+<td>Functions for manipulating, displaying, and extracting information from objects of the 'pomp' class</td></tr>
+<tr><td width="25%"><a href="pomp.html">data.frame-pomp</a></td>
+<td>Constructor of the basic POMP object</td></tr>
+<tr><td width="25%"><a href="eulermultinom.html">deulermultinom</a></td>
+<td>The Euler-multinomial distributions and Gamma white-noise processes</td></tr>
+<tr><td width="25%"><a href="plugins.html">discrete.time.sim</a></td>
+<td>Plug-ins for state-process models</td></tr>
+<tr><td width="25%"><a href="lowlevel.html">dmeasure</a></td>
+<td>pomp low-level interface</td></tr>
+<tr><td width="25%"><a href="lowlevel.html">dmeasure-method</a></td>
+<td>pomp low-level interface</td></tr>
+<tr><td width="25%"><a href="lowlevel.html">dmeasure-pomp</a></td>
+<td>pomp low-level interface</td></tr>
+<tr><td width="25%"><a href="lowlevel.html">dprior</a></td>
+<td>pomp low-level interface</td></tr>
+<tr><td width="25%"><a href="lowlevel.html">dprior-method</a></td>
+<td>pomp low-level interface</td></tr>
+<tr><td width="25%"><a href="lowlevel.html">dprior-pomp</a></td>
+<td>pomp low-level interface</td></tr>
+<tr><td width="25%"><a href="lowlevel.html">dprocess</a></td>
+<td>pomp low-level interface</td></tr>
+<tr><td width="25%"><a href="lowlevel.html">dprocess-method</a></td>
+<td>pomp low-level interface</td></tr>
+<tr><td width="25%"><a href="lowlevel.html">dprocess-pomp</a></td>
+<td>pomp low-level interface</td></tr>
+</table>
+
+<h2><a name="E">-- E --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="pfilter.html">eff.sample.size</a></td>
+<td>Particle filter</td></tr>
+<tr><td width="25%"><a href="pfilter.html">eff.sample.size-method</a></td>
+<td>Particle filter</td></tr>
+<tr><td width="25%"><a href="pfilter.html">eff.sample.size-pfilterd.pomp</a></td>
+<td>Particle filter</td></tr>
+<tr><td width="25%"><a href="plugins.html">euler.sim</a></td>
+<td>Plug-ins for state-process models</td></tr>
+<tr><td width="25%"><a href="sir.html">euler.sir</a></td>
+<td>Compartmental epidemiological models</td></tr>
+<tr><td width="25%"><a href="eulermultinom.html">eulermultinom</a></td>
+<td>The Euler-multinomial distributions and Gamma white-noise processes</td></tr>
+<tr><td width="25%"><a href="example.html">Example pomp models</a></td>
+<td>Examples of the construction of POMP models</td></tr>
+</table>
+
+<h2><a name="F">-- F --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="pfilter.html">filter.mean</a></td>
+<td>Particle filter</td></tr>
+<tr><td width="25%"><a href="pfilter.html">filter.mean-method</a></td>
+<td>Particle filter</td></tr>
+<tr><td width="25%"><a href="pfilter.html">filter.mean-pfilterd.pomp</a></td>
+<td>Particle filter</td></tr>
+</table>
+
+<h2><a name="G">-- G --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="plugins.html">gillespie.sim</a></td>
+<td>Plug-ins for state-process models</td></tr>
+<tr><td width="25%"><a href="sir.html">gillespie.sir</a></td>
+<td>Compartmental epidemiological models</td></tr>
+<tr><td width="25%"><a href="gompertz.html">gompertz</a></td>
+<td>Gompertz model with log-normal observations.</td></tr>
+</table>
+
+<h2><a name="I">-- I --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="lowlevel.html">init.state</a></td>
+<td>pomp low-level interface</td></tr>
+<tr><td width="25%"><a href="lowlevel.html">init.state-method</a></td>
+<td>pomp low-level interface</td></tr>
+<tr><td width="25%"><a href="lowlevel.html">init.state-pomp</a></td>
+<td>pomp low-level interface</td></tr>
+</table>
+
+<h2><a name="L">-- L --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="mif.html">logLik-method</a></td>
+<td>Maximum likelihood by iterated filtering</td></tr>
+<tr><td width="25%"><a href="nlf.html">logLik-method</a></td>
+<td>Parameter estimation my maximum simulated quasi-likelihood (nonlinear forecasting)</td></tr>
+<tr><td width="25%"><a href="pfilter.html">logLik-method</a></td>
+<td>Particle filter</td></tr>
+<tr><td width="25%"><a href="pmcmc.html">logLik-method</a></td>
+<td>The particle Markov chain Metropolis-Hastings algorithm</td></tr>
+<tr><td width="25%"><a href="probe.html">logLik-method</a></td>
+<td>Probe a partially-observed Markov process by computing summary statistics and the synthetic likelihood.</td></tr>
+<tr><td width="25%"><a href="traj-match.html">logLik-method</a></td>
+<td>Parameter estimation by fitting the trajectory of a model's deterministic skeleton to data</td></tr>
+<tr><td width="25%"><a href="mif.html">logLik-mif</a></td>
+<td>Maximum likelihood by iterated filtering</td></tr>
+<tr><td width="25%"><a href="nlf.html">logLik-nlfd.pomp</a></td>
+<td>Parameter estimation my maximum simulated quasi-likelihood (nonlinear forecasting)</td></tr>
+<tr><td width="25%"><a href="pfilter.html">logLik-pfilterd.pomp</a></td>
+<td>Particle filter</td></tr>
+<tr><td width="25%"><a href="pmcmc.html">logLik-pmcmc</a></td>
+<td>The particle Markov chain Metropolis-Hastings algorithm</td></tr>
+<tr><td width="25%"><a href="probe.html">logLik-probed.pomp</a></td>
+<td>Probe a partially-observed Markov process by computing summary statistics and the synthetic likelihood.</td></tr>
+<tr><td width="25%"><a href="traj-match.html">logLik-traj.matched.pomp</a></td>
+<td>Parameter estimation by fitting the trajectory of a model's deterministic skeleton to data</td></tr>
+<tr><td width="25%"><a href="logmeanexp.html">logmeanexp</a></td>
+<td>The log-mean-exp trick</td></tr>
+<tr><td width="25%"><a href="LondonYorke.html">LondonYorke</a></td>
+<td>Historical childhood disease incidence data</td></tr>
+</table>
+
+<h2><a name="M">-- M --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="pomp.html">matrix-pomp</a></td>
+<td>Constructor of the basic POMP object</td></tr>
+<tr><td width="25%"><a href="proposals.html">MCMC proposal distributions</a></td>
+<td>MCMC proposal distributions</td></tr>
+<tr><td width="25%"><a href="proposals.html">MCMC proposal functions</a></td>
+<td>MCMC proposal distributions</td></tr>
+<tr><td width="25%"><a href="mif.html">mif</a></td>
+<td>Maximum likelihood by iterated filtering</td></tr>
+<tr><td width="25%"><a href="mif.html">mif-class</a></td>
+<td>Maximum likelihood by iterated filtering</td></tr>
+<tr><td width="25%"><a href="mif.html">mif-method</a></td>
+<td>Maximum likelihood by iterated filtering</td></tr>
+<tr><td width="25%"><a href="mif.html">mif-methods</a></td>
+<td>Maximum likelihood by iterated filtering</td></tr>
+<tr><td width="25%"><a href="mif.html">mif-mif</a></td>
+<td>Maximum likelihood by iterated filtering</td></tr>
+<tr><td width="25%"><a href="mif.html">mif-pfilterd.pomp</a></td>
+<td>Maximum likelihood by iterated filtering</td></tr>
+<tr><td width="25%"><a href="mif.html">mif-pomp</a></td>
+<td>Maximum likelihood by iterated filtering</td></tr>
+<tr><td width="25%"><a href="mif.html">mifList-class</a></td>
+<td>Maximum likelihood by iterated filtering</td></tr>
+<tr><td width="25%"><a href="proposals.html">mvn.diag.rw</a></td>
+<td>MCMC proposal distributions</td></tr>
+<tr><td width="25%"><a href="proposals.html">mvn.rw</a></td>
+<td>MCMC proposal distributions</td></tr>
+</table>
+
+<h2><a name="N">-- N --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="nlf.html">nlf</a></td>
+<td>Parameter estimation my maximum simulated quasi-likelihood (nonlinear forecasting)</td></tr>
+<tr><td width="25%"><a href="nlf.html">nlf-method</a></td>
+<td>Parameter estimation my maximum simulated quasi-likelihood (nonlinear forecasting)</td></tr>
+<tr><td width="25%"><a href="nlf.html">nlf-nlfd.pomp</a></td>
+<td>Parameter estimation my maximum simulated quasi-likelihood (nonlinear forecasting)</td></tr>
+<tr><td width="25%"><a href="nlf.html">nlf-pomp</a></td>
+<td>Parameter estimation my maximum simulated quasi-likelihood (nonlinear forecasting)</td></tr>
+<tr><td width="25%"><a href="nlf.html">nlfd.pomp-class</a></td>
+<td>Parameter estimation my maximum simulated quasi-likelihood (nonlinear forecasting)</td></tr>
+<tr><td width="25%"><a href="nlf.html">Nonlinear forecasting</a></td>
+<td>Parameter estimation my maximum simulated quasi-likelihood (nonlinear forecasting)</td></tr>
+<tr><td width="25%"><a href="pomp.html">numeric-pomp</a></td>
+<td>Constructor of the basic POMP object</td></tr>
+</table>
+
+<h2><a name="O">-- O --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="pomp-methods.html">obs</a></td>
+<td>Functions for manipulating, displaying, and extracting information from objects of the 'pomp' class</td></tr>
+<tr><td width="25%"><a href="pomp-methods.html">obs-method</a></td>
+<td>Functions for manipulating, displaying, and extracting information from objects of the 'pomp' class</td></tr>
+<tr><td width="25%"><a href="pomp-methods.html">obs-pomp</a></td>
+<td>Functions for manipulating, displaying, and extracting information from objects of the 'pomp' class</td></tr>
+<tr><td width="25%"><a href="plugins.html">onestep.dens</a></td>
+<td>Plug-ins for state-process models</td></tr>
+<tr><td width="25%"><a href="plugins.html">onestep.sim</a></td>
+<td>Plug-ins for state-process models</td></tr>
+<tr><td width="25%"><a href="ou2.html">ou2</a></td>
+<td>Two-dimensional discrete-time Ornstein-Uhlenbeck process</td></tr>
+</table>
+
+<h2><a name="P">-- P --</a></h2>
+
+<table width="100%">
+<tr><td width="25%"><a href="parmat.html">parmat</a></td>
+<td>Create a matrix of parameters</td></tr>
+<tr><td width="25%"><a href="pfilter.html">particle filter</a></td>
+<td>Particle filter</td></tr>
+<tr><td width="25%"><a href="pomp-methods.html">partrans</a></td>
+<td>Functions for manipulating, displaying, and extracting information from objects of the 'pomp' class</td></tr>
+<tr><td width="25%"><a href="pomp-methods.html">partrans-method</a></td>
+<td>Functions for manipulating, displaying, and extracting information from objects of the 'pomp' class</td></tr>
+<tr><td width="25%"><a href="pomp-methods.html">partrans-pomp</a></td>
+<td>Functions for manipulating, displaying, and extracting information from objects of the 'pomp' class</td></tr>
+<tr><td width="25%"><a href="bsplines.html">periodic.bspline.basis</a></td>
+<td>B-spline bases</td></tr>
+<tr><td width="25%"><a href="pfilter.html">pfilter</a></td>
+<td>Particle filter</td></tr>
+<tr><td width="25%"><a href="pfilter.html">pfilter-method</a></td>
+<td>Particle filter</td></tr>
+<tr><td width="25%"><a href="pfilter.html">pfilter-pfilterd.pomp</a></td>
+<td>Particle filter</td></tr>
+<tr><td width="25%"><a href="pfilter.html">pfilter-pomp</a></td>
+<td>Particle filter</td></tr>
+<tr><td width="25%"><a href="pfilter.html">pfilterd.pomp-class</a></td>
+<td>Particle filter</td></tr>
+<tr><td width="25%"><a href="abc.html">plot-abc</a></td>
+<td>Estimation by approximate Bayesian computation (ABC)</td></tr>
+<tr><td width="25%"><a href="abc.html">plot-abcList</a></td>
+<td>Estimation by approximate Bayesian computation (ABC)</td></tr>
+<tr><td width="25%"><a href="bsmc.html">plot-bsmcd.pomp</a></td>
+<td>The Liu and West Bayesian particle filter</td></tr>
+<tr><td width="25%"><a href="abc.html">plot-method</a></td>
+<td>Estimation by approximate Bayesian computation (ABC)</td></tr>
+<tr><td width="25%"><a href="bsmc.html">plot-method</a></td>
+<td>The Liu and West Bayesian particle filter</td></tr>
+<tr><td width="25%"><a href="mif.html">plot-method</a></td>
+<td>Maximum likelihood by iterated filtering</td></tr>
+<tr><td width="25%"><a href="pmcmc.html">plot-method</a></td>
+<td>The particle Markov chain Metropolis-Hastings algorithm</td></tr>
+<tr><td width="25%"><a href="pomp-methods.html">plot-method</a></td>
+<td>Functions for manipulating, displaying, and extracting information from objects of the 'pomp' class</td></tr>
+<tr><td width="25%"><a href="probe.html">plot-method</a></td>
+<td>Probe a partially-observed Markov process by computing summary statistics and the synthetic likelihood.</td></tr>
+<tr><td width="25%"><a href="mif.html">plot-mif</a></td>
+<td>Maximum likelihood by iterated filtering</td></tr>
+<tr><td width="25%"><a href="mif.html">plot-mifList</a></td>
+<td>Maximum likelihood by iterated filtering</td></tr>
+<tr><td width="25%"><a href="pmcmc.html">plot-pmcmc</a></td>
+<td>The particle Markov chain Metropolis-Hastings algorithm</td></tr>
+<tr><td width="25%"><a href="pmcmc.html">plot-pmcmcList</a></td>
+<td>The particle Markov chain Metropolis-Hastings algorithm</td></tr>
+<tr><td width="25%"><a href="pomp-methods.html">plot-pomp</a></td>
+<td>Functions for manipulating, displaying, and extracting information from objects of the 'pomp' class</td></tr>
+<tr><td width="25%"><a href="probe.html">plot-probe.matched.pomp</a></td>
+<td>Probe a partially-observed Markov process by computing summary statistics and the synthetic likelihood.</td></tr>
+<tr><td width="25%"><a href="probe.html">plot-probed.pomp</a></td>
+<td>Probe a partially-observed Markov process by computing summary statistics and the synthetic likelihood.</td></tr>
+<tr><td width="25%"><a href="probe.html">plot-spect.pomp</a></td>
+<td>Probe a partially-observed Markov process by computing summary statistics and the synthetic likelihood.</td></tr>
+<tr><td width="25%"><a href="plugins.html">plugins</a></td>
+<td>Plug-ins for state-process models</td></tr>
+<tr><td width="25%"><a href="pmcmc.html">pmcmc</a></td>
+<td>The particle Markov chain Metropolis-Hastings algorithm</td></tr>
+<tr><td width="25%"><a href="pmcmc.html">pmcmc-class</a></td>
+<td>The particle Markov chain Metropolis-Hastings algorithm</td></tr>
+<tr><td width="25%"><a href="pmcmc.html">pmcmc-method</a></td>
+<td>The particle Markov chain Metropolis-Hastings algorithm</td></tr>
+<tr><td width="25%"><a href="pmcmc.html">pmcmc-methods</a></td>
+<td>The particle Markov chain Metropolis-Hastings algorithm</td></tr>
+<tr><td width="25%"><a href="pmcmc.html">pmcmc-pfilterd.pomp</a></td>
+<td>The particle Markov chain Metropolis-Hastings algorithm</td></tr>
+<tr><td width="25%"><a href="pmcmc.html">pmcmc-pmcmc</a></td>
+<td>The particle Markov chain Metropolis-Hastings algorithm</td></tr>
+<tr><td width="25%"><a href="pmcmc.html">pmcmc-pomp</a></td>
+<td>The particle Markov chain Metropolis-Hastings algorithm</td></tr>
+<tr><td width="25%"><a href="pmcmc.html">pmcmcList-class</a></td>
+<td>The particle Markov chain Metropolis-Hastings algorithm</td></tr>
+<tr><td width="25%"><a href="pomp.html">pomp</a></td>
+<td>Constructor of the basic POMP object</td></tr>
+<tr><td width="25%"><a href="pomp.html">pomp constructor</a></td>
+<td>Constructor of the basic POMP object</td></tr>
+<tr><td width="25%"><a href="lowlevel.html">pomp low-level interface</a></td>
+<td>pomp low-level interface</td></tr>
+<tr><td width="25%"><a href="pomp-methods.html">pomp methods</a></td>
+<td>Functions for manipulating, displaying, and extracting information from objects of the 'pomp' class</td></tr>
+<tr><td width="25%"><a href="pomp-package.html">pomp package</a></td>
+<td>Inference for partially observed Markov processes</td></tr>
+<tr><td width="25%"><a href="simulate-pomp.html">POMP simulation</a></td>
+<td>Simulations of a partially-observed Markov process</td></tr>
+<tr><td width="25%"><a href="pomp.html">pomp-class</a></td>
+<td>Constructor of the basic POMP object</td></tr>
+<tr><td width="25%"><a href="pomp.html">pomp-method</a></td>
+<td>Constructor of the basic POMP object</td></tr>
+<tr><td width="25%"><a href="pomp-methods.html">pomp-methods</a></td>
+<td>Functions for manipulating, displaying, and extracting information from objects of the 'pomp' class</td></tr>
+<tr><td width="25%"><a href="pomp.html">pomp-pomp</a></td>
+<td>Constructor of the basic POMP object</td></tr>
+<tr><td width="25%"><a href="example.html">pompExample</a></td>
+<td>Examples of the construction of POMP models</td></tr>
+<tr><td width="25%"><a href="lowlevel.html">pompLoad</a></td>
+<td>pomp low-level interface</td></tr>
+<tr><td width="25%"><a href="lowlevel.html">pompLoad-method</a></td>
+<td>pomp low-level interface</td></tr>
+<tr><td width="25%"><a href="lowlevel.html">pompLoad-pomp</a></td>
+<td>pomp low-level interface</td></tr>
+<tr><td width="25%"><a href="lowlevel.html">pompUnload</a></td>
+<td>pomp low-level interface</td></tr>
+<tr><td width="25%"><a href="lowlevel.html">pompUnload-method</a></td>
+<td>pomp low-level interface</td></tr>
+<tr><td width="25%"><a href="lowlevel.html">pompUnload-pomp</a></td>
+<td>pomp low-level interface</td></tr>
+<tr><td width="25%"><a href="spect.html">Power spectrum computation and matching</a></td>
+<td>Power spectrum computation and spectrum-matching for partially-observed Markov processes</td></tr>
+<tr><td width="25%"><a href="spect.html">power spectrum computation and matching</a></td>
+<td>Power spectrum computation and spectrum-matching for partially-observed Markov processes</td></tr>
+<tr><td width="25%"><a href="pfilter.html">pred.mean</a></td>
+<td>Particle filter</td></tr>
+<tr><td width="25%"><a href="pfilter.html">pred.mean-method</a></td>
+<td>Particle filter</td></tr>
+<tr><td width="25%"><a href="pfilter.html">pred.mean-pfilterd.pomp</a></td>
+<td>Particle filter</td></tr>
+<tr><td width="25%"><a href="pfilter.html">pred.var</a></td>
+<td>Particle filter</td></tr>
+<tr><td width="25%"><a href="pfilter.html">pred.var-method</a></td>
+<td>Particle filter</td></tr>
+<tr><td width="25%"><a href="pfilter.html">pred.var-pfilterd.pomp</a></td>
+<td>Particle filter</td></tr>
+<tr><td width="25%"><a href="pomp-methods.html">print-method</a></td>
+<td>Functions for manipulating, displaying, and extracting information from objects of the 'pomp' class</td></tr>
+<tr><td width="25%"><a href="pomp-methods.html">print-pomp</a></td>
+<td>Functions for manipulating, displaying, and extracting information from objects of the 'pomp' class</td></tr>
+<tr><td width="25%"><a href="probe.html">probe</a></td>
+<td>Probe a partially-observed Markov process by computing summary statistics and the synthetic likelihood.</td></tr>
+<tr><td width="25%"><a href="basic-probes.html">Probe functions</a></td>
+<td>Some useful probes for partially-observed Markov processes</td></tr>
+<tr><td width="25%"><a href="basic-probes.html">probe functions</a></td>
+<td>Some useful probes for partially-observed Markov processes</td></tr>
+<tr><td width="25%"><a href="probe.html">probe-method</a></td>
+<td>Probe a partially-observed Markov process by computing summary statistics and the synthetic likelihood.</td></tr>
+<tr><td width="25%"><a href="probe.html">probe-pomp</a></td>
+<td>Probe a partially-observed Markov process by computing summary statistics and the synthetic likelihood.</td></tr>
+<tr><td width="25%"><a href="probe.html">probe-probed.pomp</a></td>
+<td>Probe a partially-observed Markov process by computing summary statistics and the synthetic likelihood.</td></tr>
+<tr><td width="25%"><a href="basic-probes.html">probe.acf</a></td>
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/pomp -r 1131
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