NCEAS Project 11601

Unifying approaches to statistical inference in ecology

  • Aaron A. King
  • Pejman Rohani

ActivityDatesFurther Information
Working Group19th—23rd March 2007Participant List  
Working Group3rd—7th December 2007Participant List  
Working Group16th—20th June 2008Participant List  
Working Group12th—16th January 2009Participant List  
Working Group12th—16th April 2010Participant List  

Abstract
In the face of ecological complexity, it has very often proved useful to formulate mathematical models, which allow us to examine the consequences of specific sets of assumptions. While this approach has generated interesting and important ideas, progress has been frustrated by a fundamental hurdle: direct confrontation of models and data in a statistically robust way. We propose a working group aimed at overcoming this hurdle by synthesizing numerous state-of-the-art techniques. The approaches we will consider explicitly take into account common causes of mismatch between models and data such as process noise (demographic and environmental stochasticity), measurement error, unobserved variables, and nonstationarity. The end result of this working group will be a thorough review of the strengths and weaknesses of the various approaches under different circumstances and a set of easy-to-use statistical tools for use by non-specialists.

TypeProducts of NCEAS Research
Journal Article Boots, Michael; Childs, Dylan; Reuman, Daniel; Mealor, Michael. 2009. Local interactions lead to pathogen driven change to host population dynamics. Current Biology. Vol: 19. Pages 1660-1664.
Presentations Breto, Carles. 2008. Presentation n. Joint Statistical Meeting, August 2008. Denver, Colorado.
Journal Article Breto, Carles; He, D.; King, Aaron A.; Ionides, Edward. 2009. Time series analysis via mechanistic models. Annals of Applied Statistics. Vol: 3(1). Pages 319-348.
Journal Article Breto, Carles; Ionides, Edward. 2011. Compound Markov counting processes and their applications to modeling infinitesimally over-dispersed systems. Stochastic Processes and Their Applications. Vol: 121(11). Pages 2571-2591. (Online version)
Journal Article Chen, Shi; Fricks, John; Ferrari, Matthew. 2012. Tracking measles infection through non-linear state space models. Journal of the Royal Statistical Society Series C-Applied Statistics. Vol: 61(1). Pages 117-134. (Online version)
Journal Article Conlan, Andrew J.K.; Rohani, Pejman; Lloyd, Alun L.; Keeling, Matthew J.; Grenfell, Bryan T. 2010. Resolving the impact of waiting time distributions on the persistence of measles. Journal of the Royal Society Interface. Vol: 7(45). Pages 623-640.
Presentations Ferrari, Matthew. 2008. Presentation i. DIMACS workshop on Spatiotempral and network modeling of diseases, 2008. Tuebingen, Germany.
Presentations Ferrari, Matthew. 2008. Presentation k. Harvard School of Public Health, 2008.
Journal Article Ferrari, Matthew; Grais, R. F.; Bharti, Nita; Conlan, Andrew J.K.; Bjornstad, Ottar N.; Wolfson, L. J.; Guerin, P. J.; Djibo, A.; Grenfell, Bryan T. 2008. The dynamics of measles in sub-Saharan Africa. Nature. Vol: 451. Pages 679-684.
Journal Article He, D.; Ionides, Edward; King, Aaron A. 2010. Plug and play inference for disease dynamics: Measles in large and small towns as a case study. Journal of the Royal Society Interface. Vol: 7. Pages 271-283.
Journal Article Ionides, Edward; Breto, Carles; King, Aaron A. 2006. Inference for nonlinear dynamical systems. Proceedings of the National Academy of Sciences. Vol: 103. Pages 18438-18443.
Presentations Ionides, Edward. 2007. Presentation. University of Cambridge, Statistics group seminar, 2007.
Presentations Ionides, Edward. 2007. Presentation. Cornell University, Statistics department seminar, 2007.
Presentations Ionides, Edward. 2007. Presentation. University of St Andrews, seminar for National Centre for Statistical Ecology, 2007.
Presentations Ionides, Edward. 2007. Presentation. University of Pittsburgh, Mathematical Biology group seminar, 2007.
Presentations Ionides, Edward. 2007. Presentation. Wayne State University, Probability and Statistics group seminar, 2007.
Presentations Ionides, Edward. 2007. Presentation. University of Oxford, Statistics department seminar, 2007.
Presentations Ionides, Edward. 2007. Presentation. Pennsylvania State University, Statistics department seminar, 2007.
Presentations Ionides, Edward. 2007. Presentation. Pennsylvania State University, Center for Infectious Disease Dynamics, 2007.
Presentations Ionides, Edward. 2007. Presentation. Workshop on Statistical Methods for Modeling Dynamic Systems, 2007. Montreal, Canada.
Book Chapter Ionides, Edward; Breto, Carles; King, Aaron A. 2008. Modeling disease dynamics: Cholera as a case study. Edited by A. Biswas, S. Datta, J. Fine, M. Segal Statistical Advances in the Biomedical Sciences. Vol: Ch. 8.
Presentations Ionides, Edward. 2008. Presentation. University of Cambridge Department of Applied Mathematics and Mathematical Physics, Mathematical Biology group seminar, 2008.
Presentations Ionides, Edward. 2008. Presentation. Joint Statistical Meeting, August 2008. Denver, Colorado.
Presentations Ionides, Edward. 2008. Presentation a. Pennsylvania State University, Center for Infectious Disease Dynamics, workshop on epidemic model hierarchies and model validation, 2008.
Presentations Ionides, Edward. 2008. Presentation d. Duke University, Computational Biology /& Bioinformatics seminar, 2008.
Presentations Ionides, Edward. 2008. Presentation f. Workshop on Sequential Monte Carlo at SAMSI, 2008. North Carolina.
Presentations Ionides, Edward. 2008. Presentation g. Columbia University, Statistics department seminar, 2008.
Presentations Ionides, Edward. 2008. Presentation h. University of Cambridge Department of Engineering, Signal Processing group seminar, 2008.
Journal Article Ionides, Edward; Bhadra, A.; King, Aaron A. Iterated filtering. Journal of the Royal Statistical Society Series B-Statistical Methodology.
Presentations King, Aaron A. 2007. Presentation. Department of Epidemiology, University of Michigan, 2007. Tucson, Arizona.
Presentations King, Aaron A. 2007. Presentation. National Center for Ecological Analysis and Synthesis, 2007. Santa Barbara.
Presentations King, Aaron A. 2007. Presentation. Applied and Interdisciplinary Mathematics Program, University of Michigan, 2007. Arbor, Michigan.
Presentations King, Aaron A. 2007. Presentation. Ecology Society of America Annual Meeting, 2007. San Jose, California.
Presentations King, Aaron A. 2007. Presentation. Department of Biology, Case Western Reserve University, 2007. Cleveland, Ohio.
Presentations King, Aaron A. 2007. Presentation. Mathematical Modeling and Analysis of Populations in Biological Systems Conference, 2007. Tucson, Arizona.
Journal Article King, Aaron A.; Ionides, Edward; Pascual, Mercedes; Bouma, Menno J. 2008. Inapparent infections and cholera dynamics. Nature. Vol: 454. Pages 877-880.
Presentations King, Aaron A. 2008. Presentation. Department of Mathematics, University of California, Berkeley, 2008.
Presentations King, Aaron A. 2008. Presentation c. Department of Infectious Diseases, University of Georgia, February, 2008.
Presentations King, Aaron A. 2008. Presentation j. Ecology Society of America Annual Meeting, 2008. Milwaukee, Wisconsin.
Software King, Aaron A. Two algorithms for the POMP package.
Journal Article Mantilla-Beniers, Natalia B.; Bjornstad, Ottar N.; Grenfell, Bryan T.; Rohani, Pejman. 2010. Decreasing stochasticity through enhanced seasonality in measles epidemics. Journal of the Royal Society Interface. Vol: 7(46). Pages 727-739.
Presentations Newman, Ken B. 2008. Presentation m. Joint Statistical Meeting, Denver, Colorado, August 2008.
Journal Article Newman, Ken B.; Fernández, C.; Thomas, Len; Buckland, S. T. 2009. Monte Carlo inference for state-space models of wild animal populations. Biometrics. Vol: 65. Pages 572-583.
Presentations Reuman, Daniel. 2007. Presentation. Department of Animal and Plant Sciences, University of Sheffield, 22 November 2007. Sheffield, UK.
Journal Article Reuman, Daniel; Costantino, Robert F.; Desharnais, Robert A.; Cohen, J. E. 2008. Colour of environmental noise affects the nonlinear dynamics of cycling, stage-structured populations. Ecology Letters. Vol: 11. Pages 820-830.
Presentations Reuman, Daniel. 2008. Presentation b. Center for Population Biology, Imperial College London, 4 February 2008. London.
Presentations Reuman, Daniel. 2009. Presentation. Department of Zoology, University of Florida, 20, 22 January 2009. Gainesville, Florida.
Presentations Reuman, Daniel. 2009. Presentation. School of Biological Sciences, Royal Holloway University of London, 18 February 2009. London.
Presentations Rohani, Pejman. 2008. Presentation. Department of Biology, University of North Carolina, April 2008.
Presentations Rohani, Pejman. 2008. Presentation e. Department of Avian Health, University of Georgia, Nov 2008.
Presentations Rohani, Pejman. 2008. Presentation l. Centers for Disease Control and Prevention, Dec 2008.
Presentations Rohani, Pejman. 2008. Presentation o. Department of Infectious Diseases, University of Georgia, Feb 2008.
Presentations Rohani, Pejman. 2009. Presentation. Institute of Complex Systems, Ecole Normal Supererior, Jan 2009. Paris, France.
Journal Article Sourya, Shrestha; King, Aaron A.; Rohani, Pejman. 2011. Statistical inference for multi-pathogen systems. PLoS Computational Biology. Vol: 7(8). Pages e1002135-e1002135. (Online version)
Presentations Wearing, Helen. 2008. Presentation p. University of New Mexico, 2008.
Journal Article Wearing, Helen; Rohani, Pejman. 2009. Estimating the duration of pertussis immunity using epidemiological signatures. PLoS Pathogens. Vol: 5(10). Pages e1000647-e1000647.