[Pomp-commits] r298 - www/content
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Aug 24 12:42:14 CEST 2010
Author: kingaa
Date: 2010-08-24 12:42:14 +0200 (Tue, 24 Aug 2010)
New Revision: 298
Modified:
www/content/about.htm
www/content/pomp.bib
www/content/refs.htm
www/content/refs.tex
Log:
- add probe & spect methods & references
Modified: www/content/about.htm
===================================================================
--- www/content/about.htm 2010-08-23 18:46:42 UTC (rev 297)
+++ www/content/about.htm 2010-08-24 10:42:14 UTC (rev 298)
@@ -1,31 +1,63 @@
-<p><strong>pomp</strong> provides a very general realization of nonlinear partially-observed Markov processes (AKA state-space models, nonlinear stochastic dynamical systems). One specifies a model's process and measurement components; the package uses these functions in algorithms to simulate, analyze, and fit the model to data.</p>
-
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+<head>
+<meta name="generator" content="Bluefish 1.0.7">
+<title></title>
+</head>
+<body>
+<p><strong>pomp</strong> provides a very general realization of
+nonlinear partially-observed Markov processes (AKA state-space
+models, nonlinear stochastic dynamical systems). One specifies a
+model's process and measurement components; the package uses these
+functions in algorithms to simulate, analyze, and fit the model to
+data.</p>
<p>At the moment, support is provided for</p>
-
<ul>
- <li>basic particle filtering (AKA sequential importance sampling or sequential Monte Carlo),</li>
-
- <li>trajectory matching,</li>
-
- <li>the approximate Bayesian sequential Monte Carlo algorithm of Liu & West (2001),</li>
-
- <li>the particle Markov chain Monte Carlo method of Andrieu et al. (2010),</li>
-
- <li>the iterated filtering method of Ionides, Breto, & King (2006), and</li>
-
- <li>the nonlinear forecasting method of Ellner & Kendall.</li>
-</ul>Future support for a variety of other algorithms is envisioned. A working group of the <a href="http://nceas.ucsb.edu">National Center for Ecological Analysis and Synthesis (NCEAS)</a>, "Inference for Mechanistic Models", is currently implementing additional methods for this package.
-
-<p>Simple worked examples are provided in <a href="http://cran.at.r-project.org/web/packages/pomp/vignettes/">vignettes</a> and in the <tt>examples</tt> directory of the installed package.</p>
-
-<p>The package is provided under the GPL. Contributions are welcome, as are comments, suggestions, examples, and bug reports. Please send these to <tt>kingaa at umich dot edu</tt>.</p>
-
-<p>To keep abreast of new developments, <a href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/pomp-announce" target="_top">subscribe to the <i>pomp-announce</i> mailing list</a>.</p>
-
+<li>basic particle filtering (AKA sequential importance sampling or
+sequential Monte Carlo),</li>
+<li>trajectory matching,</li>
+<li>the approximate Bayesian sequential Monte Carlo algorithm of
+Liu & West (2001),</li>
+<li>the particle Markov chain Monte Carlo method of Andrieu et
+al. (2010),</li>
+<li>the iterated filtering method of
+Ionides, Breto, & King (2006),</li>
+<li>the nonlinear forecasting method of
+Ellner & Kendall,</li>
+<li>probe-matching methods (e.g., Kendall et al. 1999), and</li>
+<li>power-spectrum-matching methods of Reuman et al. (2006).</li>
+</ul>
+Future support for a variety of other algorithms is envisioned. A
+working group of the <a href=
+"http://nceas.ucsb.edu">National Center for Ecological Analysis and Synthesis (NCEAS)</a>,
+"Inference for Mechanistic Models", is currently implementing
+additional methods for this package.
+<p>Simple worked examples are provided in <a href=
+"http://cran.at.r-project.org/web/packages/pomp/vignettes/">vignettes</a>
+and in the <tt>examples</tt> directory of the installed
+package.</p>
+<p>The package is provided under the GPL. Contributions are
+welcome, as are comments, suggestions, examples, and bug reports.
+Please send these to <tt>kingaa at umich dot edu</tt>.</p>
+<p>To keep abreast of new developments, <a href=
+"https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/pomp-announce"
+target="_top">subscribe to the <i>pomp-announce</i> mailing
+list</a>.</p>
<table>
- <tr>
- <td><a href="http://www.nsf.gov"><img src="graphics/NSF_logo.jpg" alt="link to NSF"></a></td>
-
- <td>The development of this package has been made possible by support from the U.S. National Science Foundation (Grants #EF-0545276, #EF-0430120), by the "Inference for Mechanistic Models" Working Group supported by the National Center for Ecological Analysis and Synthesis, a Center funded by N.S.F. (Grant #DEB-0553768), the University of California, Santa Barbara, and the State of California, and by the RAPIDD program of the Science & Technology Directorate, Department of Homeland Security and the Fogarty International Center, U.S. National Institutes of Health.</td>
- </tr>
+<tr>
+<td><a href="http://www.nsf.gov"><img src="graphics/NSF_logo.jpg"
+alt="link to NSF"></a></td>
+<td>The development of this package has been made possible by
+support from the U.S. National Science Foundation (Grants
+#EF-0545276, #EF-0430120), by the "Inference for Mechanistic
+Models" Working Group supported by the National Center for
+Ecological Analysis and Synthesis, a Center funded by N.S.F. (Grant
+#DEB-0553768), the University of California, Santa Barbara, and the
+State of California, and by the RAPIDD program of the Science &
+Technology Directorate, Department of Homeland Security and the
+Fogarty International Center, U.S. National Institutes of
+Health.</td>
+</tr>
</table>
+</body>
+</html>
Modified: www/content/pomp.bib
===================================================================
--- www/content/pomp.bib 2010-08-23 18:46:42 UTC (rev 297)
+++ www/content/pomp.bib 2010-08-24 10:42:14 UTC (rev 298)
@@ -52,11 +52,9 @@
volume = {72},
pages = {314--315},
doi = {10.1111/j.1467-9868.2009.00736.x},
- owner = {kingaa},
textref = {Bhadra, A. (2010), Discussion of `Particle Markov chain Monte Carlo
methods' by C. Andrieu, A. Doucet and R. Holenstein, J. Roy. Stat.
- Soc B 72:314-315},
- timestamp = {2010.07.02}
+ Soc B 72:314-315}
}
@ARTICLE{Breto2009,
@@ -131,7 +129,7 @@
@ARTICLE{Gillespie1977a,
author = {D. T. Gillespie},
title = {Exact Stochastic Simulation of Coupled Chemical Reactions},
- journal = {J. Phys. Chem.},
+ journal = {Journal of Physical Chemistry},
year = {1977},
volume = {81},
pages = {2340--2361},
@@ -144,7 +142,7 @@
author = {He, Daihai and Ionides, Edward L. and King, Aaron A.},
title = {Plug-and-play inference for disease dynamics: measles in large and
small populations as a case study},
- journal = {Journal of The Royal Society Interface},
+ journal = {Journal of the Royal Society Interface},
year = {2010},
volume = {7},
pages = {271--283},
@@ -176,8 +174,7 @@
@ARTICLE{Ionides2006,
author = {E. L. Ionides and C. Bret{\'o} and Aaron A. King},
title = {Inference for nonlinear dynamical systems},
- journal = {Proceedings of the National Academy of Sciences of the United States
- of America},
+ journal = {Proceedings of the National Academy of Sciences of the U.S.A.},
year = {2006},
volume = {103},
pages = {18438--18443},
@@ -353,11 +350,23 @@
timestamp = {2009.09.22}
}
+ at ARTICLE{Reuman2006,
+ author = {Reuman, D. C. and Desharnais, R. A. and Costantino, R. F. and Ahmad,
+ O. S. and Cohen, J. E.},
+ title = {Power spectra reveal the influence of stochasticity on nonlinear
+ population dynamics},
+ journal = {Proceedings of the National Academy of Sciences of the U.S.A.},
+ year = {2006},
+ volume = {103},
+ pages = {18860--18865 },
+ url = {http://dx.doi.org/10.1073/pnas.0608571103}
+}
+
@ARTICLE{Wearing2009,
author = {Helen J Wearing and Pejman Rohani},
title = {Estimating the duration of pertussis immunity using epidemiological
signatures.},
- journal = {PLoS pathogens},
+ journal = {PLoS Pathogens},
year = {2009},
volume = {5},
pages = {e1000647},
Modified: www/content/refs.htm
===================================================================
--- www/content/refs.htm 2010-08-23 18:46:42 UTC (rev 297)
+++ www/content/refs.htm 2010-08-24 10:42:14 UTC (rev 298)
@@ -24,12 +24,12 @@
<dt><a name="He2010">He, D., E. L. Ionides, and A. A. King. 2010.</a></dt>
<dd>Plug-and-play inference for disease dynamics: measles in large and small populations as a case study.<br>
- Journal of The Royal Society Interface, <b>7</b>:271-283.<br></dd>
+ Journal of the Royal Society Interface, <b>7</b>:271-283.<br></dd>
<dt><a name="Ionides2006">Ionides, E. L., C. Bretó, and A. A. King. 2006.</a></dt>
<dd>Inference for nonlinear dynamical systems.<br>
- Proceedings of the National Academy of Sciences of the United States of America, <b>103</b>:18438-18443.<br></dd>
+ Proceedings of the National Academy of Sciences of the U.S.A., <b>103</b>:18438-18443.<br></dd>
<dt><a name="Kendall1999">Kendall, B. E., C. J. Briggs, W. W. Murdoch, P. Turchin, S. P. Ellner, E. McCauley, R. M. Nisbet, and S. N. Wood. 1999.</a></dt>
@@ -50,4 +50,9 @@
<dd>Combining parameter and state estimation in simulation-based filtering.<br>
In A. Doucet, N. de Freitas, and N. J. Gordon, editors, Sequential Monte Carlo Methods in Practice, pages 197-224. Springer, New York.<br></dd>
+
+ <dt><a name="Reuman2006">Reuman, D. C., R. A. Desharnais, R. F. Costantino, O. S. Ahmad, and J. E. Cohen. 2006.</a></dt>
+
+ <dd>Power spectra reveal the influence of stochasticity on nonlinear population dynamics.<br>
+ Proceedings of the National Academy of Sciences of the U.S.A., <b>103</b>:18860-18865.<br></dd>
</dl>
Modified: www/content/refs.tex
===================================================================
--- www/content/refs.tex 2010-08-23 18:46:42 UTC (rev 297)
+++ www/content/refs.tex 2010-08-24 10:42:14 UTC (rev 298)
@@ -15,6 +15,7 @@
\nocite{Kendall2005}
\nocite{King2008}
\nocite{Liu2001b}
+\nocite{Reuman2006}
\bibliographystyle{ecology}
\bibliography{pomp}
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