On parameter estimation in population models.

We describe methods for estimating the parameters of Markovian population processes in continuous time, thus increasing their utility in modelling real biological systems. A general approach, applicable to any finite-state continuous-time Markovian model, is presented, and this is specialised to a computationally more efficient method applicable to a class of models called density-dependent Markov population processes. We illustrate the versatility of both approaches by estimating the parameters of the stochastic SIS logistic model from simulated data. This model is also fitted to data from a population of Bay checkerspot butterfly (Euphydryas editha bayensis), allowing us to assess the viability of this population.

[1]  George H. Weiss,et al.  On the asymptotic behavior of the stochastic and deterministic models of an epidemic , 1971 .

[2]  Philip K. Pollett,et al.  Diffusion approximations for ecological models , 2001 .

[3]  Press,et al.  Class of fast methods for processing irregularly sampled or otherwise inhomogeneous one-dimensional data. , 1995, Physical review letters.

[4]  Ingemar Nåsell,et al.  Stochastic models of some endemic infections. , 2002, Mathematical biosciences.

[5]  D. Gillespie The chemical Langevin equation , 2000 .

[6]  George H. Weiss,et al.  Stochastic theory of nonlinear rate processes with multiple stationary states , 1977 .

[7]  Mark Bartlett,et al.  Deterministic and Stochastic Models for Recurrent Epidemics , 1956 .

[8]  Paul D. Feigin,et al.  Maximum likelihood estimation for continuous-time stochastic processes , 1976, Advances in Applied Probability.

[9]  N. Bailey The mathematical theory of epidemics , 1957 .

[10]  George H. Weiss,et al.  A large population approach to estimation of parameters in Markov population models , 1977 .

[11]  R. Levins Some Demographic and Genetic Consequences of Environmental Heterogeneity for Biological Control , 1969 .

[12]  A. Barbour,et al.  ASYMPTOTIC BEHAVIOUR OF A METAPOPULATION MODEL , 2003 .

[13]  M. S. Bartlett,et al.  Some Evolutionary Stochastic Processes , 1949 .

[14]  T. Kurtz Limit theorems for sequences of jump Markov processes approximating ordinary differential processes , 1971, Journal of Applied Probability.

[15]  M. Mangel,et al.  Four Facts Every Conservation Biologists Should Know about Persistence , 1994 .

[16]  Bengt Carlsson,et al.  Estimation of continuous-time AR process parameters from discrete-time data , 1999, IEEE Trans. Signal Process..

[17]  Charles J. Mode,et al.  Stochastic Processes in Epidemiology: Hiv/Aids, Other Infectious Diseases and Computers , 2000 .

[18]  G. Rybicki Notes on Gaussian Random Functions with Exponential Correlation Functions ( Ornstein-Uhlenbeck Process ) , 2005 .

[19]  J. Kingman Markov population processes , 1969, Journal of Applied Probability.

[20]  T. Kurtz Solutions of ordinary differential equations as limits of pure jump markov processes , 1970, Journal of Applied Probability.

[21]  Dirk P. Kroese,et al.  The Cross-Entropy Method: A Unified Approach to Combinatorial Optimization, Monte-Carlo Simulation and Machine Learning , 2004 .

[22]  P. K. Pollett,et al.  Approximations for the Long-Term Behavior of an Open-Population Epidemic Model , 2001 .

[23]  P. K. Pollett,et al.  Diffusion approximations for some simple chemical reaction schemes , 1992, Advances in Applied Probability.

[24]  T. Kurtz The Relationship between Stochastic and Deterministic Models for Chemical Reactions , 1972 .

[25]  D. J. Bartholomew,et al.  Continuous time diffusion models with random duration of interest , 1976 .

[26]  O. Diekmann,et al.  On the definition and the computation of the basic reproduction ratio R0 in models for infectious diseases in heterogeneous populations , 1990, Journal of mathematical biology.

[27]  Andrew D. Barbour,et al.  Quasi–stationary distributions in Markov population processes , 1976, Advances in Applied Probability.

[28]  P. Verhulst,et al.  Notice sur la loi que la population suit dans son accroissement. Correspondance Mathematique et Physique Publiee par A , 1838 .

[29]  W. J. Anderson Continuous-Time Markov Chains: An Applications-Oriented Approach , 1991 .

[30]  Damian Clancy,et al.  A stochastic SIS infection model incorporating indirect transmission , 2005 .

[31]  Willi Jäger,et al.  Biological Growth and Spread , 1980 .

[32]  J. Ross,et al.  Stochastic models for mainland-island metapopulations in static and dynamic landscapes , 2006, Bulletin of mathematical biology.

[33]  A D Barbour,et al.  Convergence of a structured metapopulation model to Levins’s model , 2004, Journal of mathematical biology.

[34]  James F. Quinn,et al.  Estimating the Effects of Scientific Study on Two Butterfly Populations , 1991, The American Naturalist.

[35]  Robijn Bruinsma,et al.  Soft order in physical systems , 1994 .

[36]  P. Foley,et al.  Predicting Extinction Times from Environmental Stochasticity and Carrying Capacity , 1994 .

[37]  A. D. Barbour,et al.  Density-dependent Markov population processes , 1980, Advances in Applied Probability.

[38]  J. Ross,et al.  A stochastic metapopulation model accounting for habitat dynamics , 2006, Journal of mathematical biology.

[39]  JERZY NEYMAN,et al.  COMPETITION PROCESSES , 2005 .

[40]  Joshua V. Ross Density dependent Markov population processes: models and methodology , 2007 .

[41]  A. D. Barbour,et al.  Asymptotic behavior of a metapopulation model , 2005 .

[42]  William Feller Die Grundlagen der Volterraschen Theorie des Kampfes ums Dasein in wahrscheinlichkeitstheoretischer Behandlung , 1939 .

[43]  A. D. Barbour,et al.  Equilibrium distributions Markov population processes , 1980 .

[44]  Philip K. Pollett,et al.  Diffusion Approximations for a Circuit Switching Network with Random Alternative Routing , 1991 .

[45]  Andrew D. Barbour,et al.  On a functional central limit theorem for Markov population processes , 1974, Advances in Applied Probability.

[46]  P. Pollett On a model for interference between searching insect parasites , 1990, The Journal of the Australian Mathematical Society. Series B. Applied Mathematics.

[47]  John F. McLaughlin,et al.  Climate change hastens population extinctions , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[48]  Roger B. Sidje,et al.  Expokit: a software package for computing matrix exponentials , 1998, TOMS.