Bibliography

Adler, F. R. 2004. Modeling the Dynamics of Life: Calculus and Probability for Life Scientists, 2d ed. Brooks/Cole, Pacific Grove, CA.

Agrawal, A. A. and M. Fishbein. 2006. Plant defense syndromes. Ecology 87:S132-S149.

Agren, G. L. and E. Bosatta. 1996. Theoretical Ecosystem Ecology: Understanding Element Cycles. Cambridge University Press, Cambridge, England.

Agresti, A. 2002. Categorical Data Analysis, 2d ed. Wiley, Hoboken, NJ.

Aitchison, J. 1986. The Statistical Analysis of Compositional Data. Chapman & Hall, New York.

Anderson, R. M. and R. M. May. 1991. Infectious Diseases of Humans: Dynamics and Control. Oxford Science Publications, Oxford, England.

Bacon, D. W. and D. G. Watts. 1971. Estimating the transition between two intersecting straight lines. Biometrika 58:525-534.

——. 1974. Using a hyperbola as a transition model to fit two-regime straight-line data. Technometrics 16:369-373.

Bailey, N. T. J. 1964. The Elements of Stochastic Processes with Applications to the Natural Sciences. Wiley, New York.

Barrowman, N. J. and R. A. Myers. 2000. Still more spawner-recruitment curves: The hockey stick and its generalizations. Canadian Journal of Fisheries and Aquatic Science 57:665-676.

Bates, D. M. and D. G. Watts. 1988. Nonlinear Regression Analysis and Its Applications. Wiley, New York.

Begon, M., J. L. Harper, and C. R. Townsend. 1996. Ecology: Individuals, Populations and Communities, 3d ed. Blackwell Science, Cambridge, MA.

Bellows, T. S. 1981. The descriptive properties of some models for density dependence. Journal of Animal Ecology 50:139-156.

Berger, J. and D. Berry. 1988. Analyzing data: Is objectivity possible? American Scientist 76:159-165.

Billheimer, D. P., P. Guttorp, and W. F. Fagan. 1998. Statistical analysis and interpretation of discrete compositional data. Technical Report 11. University of Washington. Seattle, Washington. http://www.nrcse.washington.edu/pdf/trs11_interp.pdf.

Bjrnstad, O. N. and B. T. Grenfell. 2001. Noisy clockwork: Time series analysis of population fluctuations in animals. Science 293:638-643.

Blanco, J. A., M. A. Zavala, J. B. Imbert, and F. J. Castillo. 2005. Sustainability of forest management practices: Evaluation through a simulation model of nutrient cycling. Forest Ecology and Management 213:209-228.

Bolker, B. M., S. W. Pacala, and C. Neuhauser. 2003. Spatial dynamics in model plant communities: What do we really know? American Naturalist 162: 135-148.

Bradlow, E. T., B. G. S. Hardie, and P. S. Fader. 2002. Bayesian inference for the negative binomial distribution via polynomial expansions. Journal of Computational & Graphical Statistics 11:189-201.

Brännström, A. and D. J. T. Sumpter. 2005. The role of competition and clustering in population dynamics. Proceedings of the Royal Society B 272:2065-2072.

Breslow, N. 2003. Whither PQL? UW Biostatistics Working Paper Series, no.192. http://www.bepress.com/uwbiostat/paper192.

Breslow, N. E. and D. G. Clayton. 1993. Approximate inference in generalized linear mixed models. Journal of the American Statistical Association 88:9-25.

Brown, D. H. and B. M. Bolker. 2004. The effects of disease dispersal and host clustering on the epidemic threshold in plants. Bulletin of Mathematical Biology 66:341-371.

Buckland, S. T., K. B. Newman, L. Thomas, and N. B. Kösters. 2004. State-space models for the dynamics of wild animal populations. Ecological Modelling 171:157-175.

Burnham, K. P. and D. R. Anderson. 1998. Model Selection and Inference: A Practical Information-Theoretic Approach. Springer, New York.

——. 2002. Model Selection and Multimodel Inference, 2d ed. Springer, New York.

——. 2004. Multimodel inference: understanding AIC and BIC in model selection. Sociological Methods & Research 33:261-304.

Butler, M. I. and C. W. Burns. 1993. Water mite predation on planktonic cladocera: Parallel curve analysis of functional responses. Oikos 66:5-16.

Calder, C., M. Lavine, P. Muller, and J. S. Clark. 2003. Incorporating multiple sources of stochasticity into dynamic population models. Ecology 84:1395-1402.

Canham, C. D. and M. Uriarte. 2006. Analysis of neighborhood dynamics of forest ecosystems using likelihood methods and modeling. Ecological Applications 16:62-73.

Carroll, R. J., J. D. Maca, and D. Ruppert. 1999. Nonparametric estimation in the presence of measurement errors. Biometrika 86:541-554.

Carroll, R. J., D. Ruppert, and L. W. Stefanski. 1995. Measurement Error in Nonlinear Models. Chapman and Hall, New York.

Case, T. J. 1999. An Illustrated Guide to Theoretical Ecology. Oxford University Press, New York.

Caswell, H. 2000. Matrix Population Models: Construction, Analysis and Interpretation. Sinauer, Sunderland, MA.

Celeux, G., F. Forbes, C. P. Robert, and D. M. Titterington. 2006. Deviance information criteria for missing data models. Bayesian Analysis 1:651-674.

Chambers, J. M. and T. Hastie, editors. 1992. Statistical Models in S. Wadsworth & Brooks/Cole, Pacific Grove, CA.

Chatfield, C. 1975. The Analysis of Time Series: Theory and Practice. Chapman and Hall, London.

Chen, Y. 2004. Multiple periodic solutions of delayed predator-prey systems with type IV functional responses. Nonlinear Analysis: Real World Applications 5:45-53.

Clark, C. J., J. R. Poulsen, B. M. Bolker, E. F. Connor, and V. T. Parker. 2005. Comparative seed shadows of bird-, monkey-, and wind-dispersed trees. Ecology 86:2684-2694.

Clark, J. S. 2007. Models for Ecological Data: An Introduction. Princeton University Press, Princeton, NJ.

Clark, J. S. and O. N. Bjrnstad. 2004. Population time series: Process variability, observation errors, missing values, lags, and hidden states. Ecology 85: 3140-3150.

Clark, J. S., M. Silman, R. Kern, E. Macklin, and J. Hilleris Lambers. 1999. Seed dispersal near and far: Patterns across temperate and tropical forests. Ecology 80:1475-1494.

Clarke, S. C., M. K. McAllister, E. J. Milner-Gulland, G. P. Kirwood, C. G. J. Michielsens, D. J. Agnew, E. K. Pikitch, H. Nakano, and M. S. Shivji. 2006. Global estimates of shark catches using trade records from commercial markets. Ecology Letters 9:1115-1126.

Cleveland, W. 1993. Visualizing Data. Hobart Press, Summit, NJ.

Cohen, J. E., F. Briand, and C. M. Newman. 1990. Community food webs: Data and theory. Springer-Verlag, Berlin.

Collings, J. B. 1997. The effects of the functional response on the bifurcation behavior of a mite predator-prey interaction model. Journal of Mathematical Biology 36:149-168.

Congdon, P. 2003. Applied Bayesian Modelling. Wiley, Hoboken, NJ.

Cook, J. R. and L. A. Stefanski. 1994. Simulation-extrapolation estimation in parametric measurement error models. Journal of the American Statistical Association 89:1314-1328.

Corless, R. M., G. H. Gonnet, D. E. G. Hare, D. J. Jeffrey, and D. E. Knuth. 1996. On the Lambert W function. Advances in Computational Mathematics 5:329-359.

Crawley, M. J. 2002. Statistical Computing: An Introduction to Data Analysis Using S-PLUS. Wiley, Hoboken, NJ.

——. 2005. Statistics: An Introduction Using R. Wiley, Hoboken, NJ.

——. 2007. The R Book. Wiley, Hoboken, NJ.

Cressie, N. A. C. 1991. Statistics for Spatial Data. Wiley, New York.

Crome, F. H. J. 1997. Researching tropical forest fragmentation: Shall we keep on doing what we're doing? Pages 485-501 in W. F. Laurance and R. O. Bierregard, editors. Tropical Forest Remnants: Ecology, Management, and Conservation of Fragmented Communities. University of Chicago Press, Chicago.

Crome, F. H. J., M. R. Thomas, and L. A. Moore. 1996. A novel Bayesian approach to assessing impacts of rain forest logging. Ecological Applications 6:1104-1123.

Crowder, M. J. 1978. Beta-binomial Anova for proportions. Applied Statistics 27: 34-37.

Dalgaard, P. 2003. Introductory statistics in R. Springer, New York.

Dalling, J. W., H. C. Muller-Landau, S. J. Wright, and S. P. Hubbell. 2002. Role of dispersal in the recruitment limitation of neotropical pioneer species. Journal of Ecology 90:714-727.

Damgaard, C. 1999. A test of asymmetric competition in plant monocultures using the maximum likelihood function of a simple growth model. Ecological Modelling 116:285-292.

Damgaard, C., J. Weiner, and H. Nagashima. 2002. Modelling individual growth and competition in plant populations: Growth curves of Chenopodium album at two densities. Journal of Ecology 90:666-671.

de Valpine, P. 2003. Better inferences from population-dynamics experiments using Monte Carlo state-space likelihood methods. Ecology 84:3064-3077.

de Valpine, P. and A. Hastings. 2002. Fitting population models incorporating process noise and observation error. Ecology 72:57-76.

Dennis, B. 1996. Discussion: Should ecologists become Bayesians? Ecological Applications 6:1095-1103.

Diaconis, P., S. Holmes, and R. Montgomery. 2004. Dynamical bias in the coin toss. Technical report 2004-32, Stanford University. http://www-stat.stanford.edu/reports/abstracts/04-32.pdf.

Diggle, P. J. 1990. Time Series: A Biostatistical Introduction. Oxford University Press, New York.

Doak, D. F., K. Gross, and W. F. Morris. 2005. Understanding and predicting the effects of sparse data on demographic analyses. Ecology 86:1154-1163.

Dobson, A. J. 1990. An Introduction to Generalized Linear Models. Chapman and Hall, London.

Dodd, M. E. and J. Silvertown. 2000. Size-specific fecundity and the influence of lifetime size variation upon effective population size in Abies balsamea. Heredity 85:604-609.

Doucet, A., N. de Freitas, and N. J. Gordon. 2001. Sequential Monte Carlo Methods in Practice. Springer-Verlag, New York.

Drury, K. L. S. and G. Dwyer. 2005. Combining stochastic models with experiments to understand the dynamics of monarch butterfly colonization. American Naturalist 166:731-750.

Duncan, R. S. and V. E. Duncan. 2000. Forest succession and distance from forest edge in an Afro-tropical grassland. Biotropica 32:33-41.

Dwyer, G., S. Levin, and L. Buttel. 1990. A simulation model of the population dynamics and evolution of myxomatosis. Ecological Monographs 60:423-447.

Edwards, A. W. F. 1992. Likelihood: Expanded Edition. Johns Hopkins University Press, Baltimore, MD.

Edwards, D. 1996. Comment: The first data analysis should be journalistic. Ecological Applications 6:1090-1094.

Ellison, A. M. 1996. An introduction to Bayesian inference for ecological research and environmental decision-making. Ecological Applications 6:1036-1046.

Ellner, S. P., B. A. Bailey, G. V. Bobashev, A. Gallant, B. T. Grenfell, and D. W. Nychka. 1998. Noise and nonlinearity in measles epidemics: Combining mechanistic and statistical approaches to population modeling. American Naturalist 151: 425-440.

Ellner, S. P. and J. Guckenheimer. 2006. Dynamic Models in Biology. Princeton University Press, Princeton, NJ.

Ellner, S. P., Y. Seifu, and R. H. Smith. 2002. Fitting population dynamic models to time-series data by gradient matching. Ecology 83:2256-2270.

Elston, D. A., R. Moss, T. Boulinier, C. Arrowsmith, and X. Lambin. 2001. Analysis of aggregation, a worked example: Numbers of ticks on red grouse chicks. Parasitology 122: 563-569.

Emlen, D. J. 1996. Artificial selection on horn length-body size allometry in the horned beetle Onthophagus acuminatus (Coleoptera: Scarabaeidae). Evolution 50:1219-1230.

Essington, T. E., J. F. Kitchell, and C. J. Walters. 2001. The von Bertalanffy growth function, bioenergetics, and the consumption rates of fish. Canadian Journal of Fisheries and Aquatic Science 58:2129-2138.

Etienne, R. S., M. E. F. Apol, and H. Olff. 2006a. Demystifying the West, Brown & Enquist model of the allometry of metabolism. Functional Ecology 20:394-399.

Etienne, R. S., A. M. Latimer, J. A. Silander, and R. M. Cowling. 2006b. Comment on “Neutral ecological theory reveals isolation and rapid speciation in a biodiversity hot spot.” Science 311:610b.

Evans, M., N. Hastings, and B. Peacock. 2000. Statistical Distributions, 3d ed. Wiley, New York.

Everitt, B. and T. Hothorn. 2006. A Handbook of Statistical Analyses Using R. Chapman & Hall/CRC, Boca Raton, FL.

Faraway, J. J. 2004. Linear Models with R. CRC Press, Boca Raton, FL.

——. 2006. Extending Linear Models with R: Generalized Linear, Mixed Effects and Nonparametric Regression Models. Chapman & Hall/CRC, Boca Raton, FL.

Fenner, F., M. F. Day, and G. M. Woodroffe. 1956. Epidemiological consequences of the mechanical transmission of myxomatosis by mosquitoes. Journal of Hygiene 54:284-303.

Ferrari, J. B. and S. Sugita. 1996. A spatially explicit model of leaf litter fall in hemlock-hardwood forests. Canadian Journal of Forest Research 26:1905-1913.

Finkenstadt, B. F. and B. T. Grenfell. 2000. Time series modelling of childhood diseases: A dynamical systems approach. Journal of the Royal Statistical Society Series C: Applied Statistics 49:187-205.

Flather, C. H. 1996. Fitting species-accumulation functions and assessing regional land use impacts on avian diversity. Journal of Biogeography 23:155-168.

Forsythe, G., M. Malcolm, and C. Moler. 1977. Computer Methods for Mathematical Computations. Prentice Hall, Englewood Cliffs, NJ.

Fox, J. 2002. An R and S-PLUS Companion to Applied Regression. Sage Press, Thousand Oaks, CA.

Framstad, E., N. C. Stenseth, O. N. Bjornstad, and W. Falck. 1997. Limit cycles in Norwegian lemmings: Tensions between phase-dependence and density-dependence. Proceedings: Biological Sciences 264:31-38.

Fujiwara, M., B. E. Kendall, R. M. Nisbet, and W. A. Bennett. 2005. Analysis of size trajectory data using an energetic-based growth model. Ecology 86:1441-1451.

Gani, R. and S. Leach. 2001. Transmission potential of smallpox in contemporary populations. Nature 414:748-751.

Gelman, A. 2005. Analysis of variance—Why it is more important than ever. Annals of Statistics 33:1-53.

——. 2006. Prior distributions for variance parameters in hierarchical models. Bayesian Analysis 1:515-533.

Gelman, A., J. Carlin, H. S. Stern, and D. B. Rubin. 1996. Bayesian Data Analysis. Chapman and Hall, New York.

Gelman, A. and J. Hill. 2006. Data Analysis Using Regression and Multilevel/Hierarchical Models. Cambridge University Press, Cambridge, England.

Gelman, A. and D. Nolan. 2002. You can load a die, but you can't bias a coin. American Statistician 56:308-311.

Gelman, A. and F. Tuerlinckx. 2000. Type S error rates for classical and Bayesian single and multiple comparison procedures. Computational Statistics 15: 373-390.

Gibson, G. J. 1997. Markov chain Monte Carlo methods for fitting spatiotemporal stochastic models in plant epidemiology. Journal of the Royal Statistical Society Series C 46:215-233.

Gibson, G. J. and E. Renshaw. 1998. Estimating parameters in stochastic compartmental models using Markov chain methods. IMA Journal of Mathematics Applied in Biology and Medicine 15:19-40.

——. 2001. Likelihood estimation for stochastic compartmental models using Markov chain methods. Statistics and Computing 11:347-358.

Gillespie, D. T. 1977. Exact stochastic simulation of coupled chemical reactions. Journal of Physical Chemistry 81:2340-2361.

Goldman, N. and S. Whelan. 2000. Statistical tests of gamma-distributed rate heterogeneity in models of sequence evolution in phylogenetics. Molecular Biology and Evolution 17:975-978.

Gonick, L. and W. Smith. 1993. The Cartoon Guide to Statistics. Harper-Perennial, New York.

Gotelli, N. J. 2001. A Primer of Ecology, 3d ed. Sinauer, Sunderland, MA.

Gotelli, N. J. and A. M. Ellison. 2004. A Primer of Ecological Statistics. Sinauer, Sunderland, MA.

Grenfell, B. T., K. Wilson, B. Finkenstadt, T. N. Coulson, S. Murray, S. D. Albon, J. M. Pemberton, T. H. Clutton-Brock, and M. J. Crawley. 1998. Noise and determinism in synchronized sheep dynamics. Nature 394:674-677.

Gurney, W. S. C. and R. Nisbet. 1998. Ecological Dynamics. Oxford University Press, Oxford, England.

Guthery, F. S., L. A. Brennan, M. J. Peterson, and J. J. Lusk. 2005. Invited paper: Information theory in wildlife science: Critique and viewpoint. Journal of Wildlife Management 69:457-465.

Haefner, J. W. 1996. Modeling Biological Systems: Principles and Applications. Kluwer, Dordrecht, Netherlands.

Haining, R. 2003. Spatial data analysis: Theory and practice. Cambridge University Press, Cambridge, England.

Halley, J. M., S. Hartley, A. S. Kallimanis, W. E. Kunin, J. J. Lennon, and S. P. Sgardelis. 2004. Uses and abuses of fractal methodology in ecology. Ecology Letters 7:254-271.

Hanski, I. 1999. Metapopulation Ecology. Oxford University Press, Oxford, England.

Hargrove, W. W. and J. Pickering. 1992. Pseudoreplication: A sine qua non for regional ecology. Landscape Ecology 6:251-258.

Harrison, P. J., S. T. Buckland, L. Thomas, R. Harris, P. P. Pomeroy, and J. Harwood. 2006. Incorporating movement into models of grey seal population dynamics. Journal of Animal Ecology 75:634-645.

Hassell, M. P. 1975. Density-dependence in single-species populations. Journal of Animal Ecology 45:283-296.

Hastie, T. J. and D. Pregibon. 1991. Generalized linear models. Pages 377-420 in J. M. Chambers and T. J. Hastie, editors. Statistical Models in S. Wadsworth & Brooks/Cole, Pacific Grove, CA.

Hastings, A. 1997. Population Biology: Concepts and Models. Springer-Verlag, New York.

Hatfield, J. S., W. A. Link, D. K. Dawson, and E. L. Lindquist. 1996. Coexistence and community structure of tropical trees in a Hawaiian montane rain forest. Biotropica 28:746-758.

Heffner, R. A., M. J. Butler, and C. K. Reilly. 1996. Pseudoreplication revisited. Ecology 77:2558-2562.

Heiberger, R. M. and B. Holland. 2004. Statistical Analysis and Data Display: An Intermediate Course with Examples in S-PLUS, R, and SAS. Springer, New York.

Henson, S. M., R. F. Costantino, J. M. Cushing, R. A. Desharnais, B. Dennis, and A. A. King. 2001. Lattice effects observed in chaotic dynamics of experimental populations. Science 294:602-605.

Hilborn, R. and M. Mangel. 1997. The Ecological Detective: Confronting Models with Data. Princeton University Press, Princeton, NJ.

Hoaglin, D. C., F. Mosteller, and J. W. Tukey, editors. 2000. Understanding Robust and Exploratory Data Analysis. Wiley, New York.

——. 2006. Exploring Data Tables, Trends, and Shapes, rev. ed. Wiley, New York.

Holt, R. D. 1983. Optimal foraging and the form of the predator isocline. American Naturalist 122:521-541.

Horne, J. S. and E. O. Garton. 2006. Selecting the best home range model: An information-theoretical approach. Ecology 87:1146-1152.

Hurlbert, S. 1984. Pseudoreplication and the design of ecological field experiments. Ecological Monographs 54:187-211.

Ingber, L. 1996. Adaptive simulated annealing (ASA): Lessons learned. Control and Cybernetics 25:33-54. http://www.ingber.com/asa96_lessons.pdf.

Inouye, B. D. 1999. Estimating competition coefficients: Strong competition among three species of frugivorous flies. Oecologia 120:588-594.

——. 2005. The importance of the variance around the mean effect size of ecological processes: comment. Ecology 86:262-264.

Ionides, E. L., C. Breto, and A. A. King. 2006. Inference for nonlinear dynamical systems. Proceedings of the National Academy of Sciences of the USA 103:18438-18443.

Ives, A. R., S. R. Carpenter, and B. Dennis. 1999. Community interaction webs and zooplankton responses to planktivory manipulations. Ecology 80:1405-1421.

Jang, W. and J. Lim. 2005. PQL estimation biases in generalized linear mixed models. Discussion paper 2005-21, Institute for Statistics and Decision Sciences, Duke University. http://ftp.stat.duke.edu/WorkingPapers/05-21.html.

Jeffreys, H. 1961. The Theory of Probability. Clarendon Press, Oxford, England.

Jeschke, J. M., M. Kopp, and R. Tollrain. Consumer-food systems: why type I functional responses are exclusive to filter feeders. Biological Reviews 79:337-349.

Johnson, D. J. 1999. The insignificance of statistical significance testing. Journal of Wildlife Management 63:763-772.

Johnson, J. B. and K. S. Omland. 2004. Model selection in ecology and evolution. Trends in Ecology and Evolution 19:101-108.

Jonsen, I. D., R. A. Myers, and J. M. Flemming. 2003. Meta-analysis of animal movement using state-space models. Ecology 84:3055-3063.

Juliano, S. A. 1993. Nonlinear curve fitting: predation and functional response curves. Pages 159-182 in S. M. Scheiner and J. Gurevitch, editors. Design and Analysis of Ecological Experiments. Chapman & Hall, New York.

Kass, R. E. and A. E. Raftery. 1995. Bayes factors and model uncertainty. Journal of the American Statistical Association 90:773-795.

Katz, R. W., G. S. Brush, and M. B. Parlange. 2005. Statistics of extremes: Modeling ecological disturbances. Ecology 86:112-1134.

Keeling, K. B. and R. J. Pavur. 2007. A comparative study of the reliability of nine statistical software packages. Computational Statistics & Data Analysis 51:3811-3831.

Keller, J. B. 1986. The probability of heads. American Mathematical Monthly 93:191-197.

Kendall, M. and A. Stuart. 1979. The Advanced Theory of Statistics. Vol. 2: Inference and Relationship, 4th ed. Griffin, London.

Kenward, M. G. and J. H. Roger. 1997. Small sample inference for fixed effects from restricted maximum likelihood. Biometrics 53:983-997.

Kerman, J. and A. Gelman. 2006. Tools for Bayesian data analysis in R. Statistical Computing and Graphics 17:9-13.

Kirkpatrick, S., C. Gelatt, and M. Vecchi. 1983. Optimization by simulated annealing. Science 220:671-680.

Kitakado, T., S. Kitada, H. Kishino, and H. J. Skaug. 2006. An integrated-likelihood method for estimating genetic differentiation between populations. Genetics 173:2073-2082.

Kitanidis, P. K. 1997. Introduction to geostatistics: Applications in Hydrogeology. Cambridge University Press, Cambridge, England.

Lande, R., S. Engen, and B.-E. Sather. 2003. Stochastic Population Dynamics in Ecology and Conservation. Oxford University Press, Oxford, England.

Latimer, A. M., J. A. Silander, and R. M. Cowling. 2005. Neutral ecological theory reveals isolation and rapid speciation in a biodiversity hot spot. Science 309: 1722-1725.

Lee, Y., J. A. Nelder, and Y. Pawitan 2006. Generalized Linear Models with Random Effects: Unified Analysis via H-Likelihood. Chapman & Hall/CRC, Boca Raton, FL.

Lekone, P. E. and B. F. Finkenstadt. 2006. Statistical inference in a stochastic epidemic SEIR model with control intervention: Ebola as a case study. Biometrics 62:1170-1177.

Lele, S. R., B. Dennis, and F. Lutscher. 2007. Data cloning: easy maximum likelihood estimation for complex ecological models using Bayesian Markov chain Monte Carlo methods. Ecology Letters 10:551-563.

Levins, R. 1966. The strategy of model building in population biology. American Scientist 54:421-431.

——. 1993. A response to Orzack and Sober: Formal analysis and the fluidity of science. Quarterly Review of Biology 68:547-555.

Levins, R. and D. Culver. 1971. Regional coexistence of species and competition between rare species. Proceedings of the National Academy of Sciences of the USA 6:1246-1248.

Lindley, S. T. 2003. Estimation of population growth and extinction parameters from noisy data. Ecological Applications 13:806-813.

Lindsey, J. K. 1997. Applying Generalized Linear Models. Springer, New York.

——. 1999a. Models for Repeated Measurements, 2d ed. Oxford University Press, New York.

——. 1999b. Some statistical heresies. The Statistician 48:1-40.

——. 2001. Nonlinear Models in Medical Statistics. Oxford University Press, New York.

——. 2004. Introduction to Applied Statistics: A Modelling Approach. Oxford University Press, New York.

Link, W. A. and R. J. Barker. 2006. Model weights and the foundations of multimodel inference. Ecology 87:2626-2635.

Lloyd-Smith, J. O. 2007. Maximum likelihood estimation of the negative binomial dispersion parameter for highly overdispersed data, with applications to infectious diseases. PLoS ONE 2:e180.

Ludwig, D. 1996. Uncertainty and the assessment of extinction probabilities. Ecological Applications 6:1067-1076.

Lynch, M. and B. Walsh. 1997. Genetics and Analysis of Quantitative Traits. Sinauer, Sunderland, MA.

Lyons, L. 1991. A Practical Guide to Data Analysis for Physical Science Students. Cambridge University Press, Cambridge, England.

Lytle, D. A. 2002. Flash floods and aquatic insect life-history evolution: Evaluation of multiple models. Ecology 83:370-385.

Maindonald, J. and J. Braun. 2003. Data Analysis and Graphics Using R: An Example-Based Approach. Cambridge University Press, Cambridge, England.

Mangel, M. 2006. The Theoretical Biologist's Toolbox: Quantitative Methods for Ecology and Evolutionary Biology. Cambridge University Press, Cambridge, England.

Martin, T. G., B. A. Wintle, J. R. Rhodes, P. M. Kuhnert, S. A. Field, S. A. Low-Choy, A. J. Tyre, and H. H. Possingham. 2005. Zero-tolerance ecology: Improving ecological inference by modelling the source of zero observations. Ecology Letters 8:1235-1246.

May, R. M. 1973. Stability and Complexity in Model Ecosystems. Princeton University Press, Princeton, NJ.

——. 1978. Host-parasitoid systems in patchy environments: A phenomenological model. Journal of Animal Ecology 47:833-844.

Maynard-Smith, J. and M. Slatkin. 1973. The stability of predator-prey systems. Ecology 54:384-391.

Mazerolle, M. J. 2004. Mouvements et reproduction des amphibiens en tourbieres perturbees. Ph.D. Diss. Universite Laval, Quebec. http://www.theses.ulaval.ca/2004/21842.html.

McCarthy, M. A. and K. M. Parris. 2004. Clarifying the effect of toe clipping on frogs with Bayesian statistics. Journal of Applied Ecology 41:780-786.

McCullagh, P. and J. A. Nelder. 1989. Generalized Linear Models. Chapman and Hall, London.

McCullough, B. D. and B. Wilson. 2005. On the accuracy of statistical procedures in Microsoft Excel 2003. Computational Statistics & Data Analysis 49: 1244-1252.

McGill, B. J., B. A. Maurer, and M. D. Weiser. 2006. Empirical evaluation of neutral theory. Ecology 87:1411-1423.

McKay, B., D. Bar-Natan, M. Bar-Hillel, and G. Kalai. 1999. Solving the Bible Code puzzle. Statistical Science 14:150-173.

Melbourne, B. A. and P. Chesson. 2006. The scale transition: Scaling up population dynamics with field data. Ecology 87:1478-1488.

Millar, R. B. and R. Meyer. 2000. Bayesian state-space modeling of age-structured data: Fitting a model is just the beginning. Canadian Journal of Fisheries and Aquatic Sciences 57: 43-50.

Miller, P. S. and R. C. Lacy. 2005. VORTEX. A Stochastic Simulation of the Simulation Process. Version 9.50 User's Manual. Conservation Breeding Specialist Group (IUCN/SSC), Apple Valley, MN. http://www.vortex9.org/vortex.html.

Mitzenmacher, M. 2003. A brief history of generative models for power laws and lognormal distributions. Internet Mathematics 1:226-251.

Moorcroft, P. R., M. W. Lewis, and R. L. Crabtree. 2006. Mechanistic home range patterns capture spatial patterns and dynamics of coyote territories in Yellowstone. Proceedings of the Royal Society B 273:1651-1659.

Morales, J. M., D. T. Haydon, J. Frair, K. E. Holsinger, and J. M. Fryxell. 2004. Extracting more out of relocation data: Building movement models as mixtures of random walks. Ecology 85:2436-2445.

Morris, W. F. 1997. Disentangling effects of induced plant defenses and food quantity on herbivores by fitting nonlinear models. American Naturalist 150:299-327.

Morris, W. F. and D. F. Doak. 2002. Quantitative Conservation Biology: Theory and Practice of Population Viability Analysis. Sinauer, Sunderland, MA.

Mossel, E. and E. Vigoda. 2006. Phylogenetic MCMC algorithms are misleading on mixtures of trees. Science 309:2207-2209.

Muggeo, V. M. R. 2003. Estimating regression models with unknown breakpoints. Statistics in Medicine 22:3055-3072.

Nakagawa, S. 2004. A farewell to Bonferroni: The problems of low statistical power and publication bias. Behavioral Ecology 15:1044-1045.

Nelder, J. A. 1961. The fitting of a generalization of the logistic curve. Biometrics 17:89-110.

Ness, J. H., W. F. Morris, and J. L. Bronstein. 2006. Integrating quality and quantity of mu-tualistic service to contrast ant species protecting Ferocactus wislizeni. Ecology 87:912-921.

Neuhauser, C. 2003. Calculus for Biology and Medicine, 2d ed. Prentice Hall, Upper Saddle River, NJ.

Niklas, K. J. 1993. The allometry of plant reproductive biomass and stem diameter. American Journal of Botany 80:461-467.

Nisbet, R. and W. Gurney. 1982. Modelling Fluctuating Populations. Wiley, New York. Reprint Blackburn Press, Caldwell, NJ, 2003.

Oehlert, G. W. 1992. A note on the delta method. American Statistician 46:27-29.

Oksanen, L. 2001. Logic of experiments in ecology: Is pseudoreplication a pseudoissue? Oikos 94:27-38.

Okubo, A. 1980. Diffusion and Ecological Problems: Mathematical Models. Springer-Verlag, New York.

Okuyama, T. and B. M. Bolker. 2005. Combining genetic and ecological data to estimate sea turtle origins. Ecological Applications 15:315-325.

Orzack, S. H. and E. Sober. 1993. A critical assessment of Levins's The Strategy of Model Building in Population Biology (1966). Quarterly Review of Biology 68:533-546.

Osenberg, C. W., C. M. St. Mary, R. J. Schmitt, S. J. Holbrook, P. Chesson, and B. Byrne. 2002. Rethinking ecological inference: Density dependence in reef fishes. Ecology Letters 5:715-721.

Otto, S. P. and T. Day. 2007. A Biologist's Guide to Mathematical Modeling in Ecology and Evolution. Princeton University Press, Princeton, NJ.

Ovaskainen, O. 2004. Habitat-specific movement parameters estimated using mark-recapture data and a diffusion model. Ecology 85:242-257.

Pacala, S. and J. Silander Jr. 1990. Field tests of neighborhood population dynamic models of two annual weed species. Ecological Monographs 60:113-134.

Pacala, S. W. and J. A. Silander Jr. 1987. Neighborhood interference among velvet leaf, Abutilon theophrasti, and pigweed, Amaranthus retroflexus. Oikos 48:217-224.

Paradis, E. 2006. Analysis of Phylogenetics and Evolution with R. Springer, New York.

Parris, K. M. 2006. Urban amphibian assemblages as metacommunities. Journal of Animal Ecology 75:757-764.

Pascual, M. A. and P. Kareiva. 1996. Predicting the outcome of competition using experimental data: Maximum likelihood and Bayesian approaches. Ecology 77:337-349.

Persson, L., K. Leonardsson, A. M. de Roos, M. Gyllenberg, and B. Christensen. 1998. Ontogenetic scaling of foraging rates and the dynamics of a size-structured consumer-resource model. Theoretical Population Biology 54:270-293.

Petersen, J. E., J. C. Cornwell, and W. M. Kemp. 1999. Implicit scaling in the design of experimental aquatic ecosystems. Oikos 85:3-18.

Piegorsch, W. W. 1990. Maximum likelihood estimation for the negative binomial dispersion parameter. Biometrics 46:863-867.

Pielou, E. 1977. Mathematical Ecology, 2d ed. Wiley, New York.

Pieters, E. P., C. E. Gates, J. H. Matis, and W. L. Sterling. 1977. Small sample comparison of different estimators of negative binomial parameters. Biometrics 33:718-723.

Pinheiro, J. C. and D. M. Bates. 2000. Mixed-Effects Models in S and S-PLUS. Springer, New York.

Post, E., N. C. Stenseth, R. O. Peterson, J. A. Vucetich, and A. M. Ellisa. 2002. Phase dependence and population cycles in a large-mammal predator-prey system. Ecology 83: 2997-3002.

Poulin, R. 1996. Measuring parasite aggregation: Defending the index of discrepancy. International Journal for Parasitology 26:227-229.

Press, W. H., S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery. 1994. Numerical Recipes in C: The Art of Scientific Computing. Cambridge University Press, Cambridge, England.

Quinn, G. P. and M. J. Keough. 2002. Experimental Design and Data Analysis for Biologists. Cambridge University Press, Cambridge, England.

Quinn, T. J. and R. B. Deriso. 1999. Quantitative Fish Dynamics. Oxford University Press, New York.

Raftery, A. E. and S. M. Lewis. 1996. Implementing MCMC. Pages 115-130 in W. R. Gilks, S. Richardson, and D. J. Spiegelhalter, editors. Markov Chain Monte Carlo in Practice. Chapman and Hall, London.

Rand, D. A. and H. B. Wilson. 1991. Chaotic stochasticity: A ubiquitous source of unpredictability in epidemics. Proceedings of the Royal Society B 246:6.

Reeve, J. D. and W. W. Murdoch. 1985. Aggregation by parasitoids in the successful control of the California red scale: A test of theory. Journal of Animal Ecology 54:797-816.

Renshaw, E. 1991. Modelling Biological Populations in Space and Time. Cambridge University Press, Cambridge, England.

Ribbens, E., J. A. Silander, and S. W. Pacala. 1994. Seedling recruitment in forests: Calibrating models to predict patterns of tree seedling dispersion. Ecology 75:1794-1806.

Richards, F. J. 1959. A flexible growth function for empirical use. Journal of Experimental Botany 10:290-300.

Richards, S. A. 2005. Testing ecological theory using the information-theoretic approach: Examples and cautionary results. Ecology 86:2805-2814.

Ricketts, T. H. 2001. The matrix matters: Effective isolation in fragmented landscapes. American Naturalist 158:87-99.

Ripley, B. D. 1981. Spatial Statistics. Wiley, New York.

——. 2004. Selecting amongst large classes of models. Pages 155-170 in N. Adams,

M. Crowder, D. J. Haud, and D. Stephens, editors. Methods and Models in Statistics: In Honour of Professor John Nelder, FRS. Imperial College Press, London.

Rogers, D. J. 1972. Random search and insect population models. Journal of Animal Ecology 41:369-383.

Ronquist, F., B. Larget, J. P. Huelsenbeck, J. P. Kadane, D. Simon, and P. van der Mark. 2006. Comment on “Phylogenetic MCMC algorithms are misleading on mixtures of trees.” Science 312:3767a.

Rosenheim, J. A. and D. Rosen. 1991. Foraging and oviposition decisions in the parasitoid Aphytis lingnanensis: Distinguishing the influences of egg load and experience. Journal of Animal Ecology 60:873-893.

Roughgarden, J. 1997. Primer of Ecological Theory. Prentice Hall, Upper Saddle River, NJ.

Royama, T. 1992. Analytical Population Dynamics. Chapman and Hall, New York.

Ruel, J.J. and M. P. Ayres. 1999. Jensen's inequality predicts effects of environmental variation. Trends in Ecology and Evolution 14:361-366.

Sack, L., P. J. Melcher, W. H. Liu, E. Middleton, and T. Pardee. 2006. How strong is intracanopy leaf plasticity in temperate deciduous trees? American Journal of Botany 93: 829839.

Saha, K. and S. Paul. 2005. Bias-corrected maximum likelihood estimator of the negative binomial dispersion parameter. Biometrics 61:179-185.

Sandin, S. A. and S. W. Pacala. 2005. Fish aggregation results in inversely density-dependent predation on continuous coral reefs. Ecology 86:1520-1530.

Scheiner, S. M. and J. Gurevitch, editors. 2001. Design and Analysis of Ecological Experiments, 2d ed. Chapman and Hall, New York.

Schmitt, R. J., S. J. Holbrook, and C. W. Osenberg. 1999. Quantifying the effects of multiple processes on local abundance: A cohort approach for open populations. Ecology Letters 2:294-303.

Schnute, J. 1981. A versatile growth model with statistically stable parameters. Canadian Journal of Fisheries and Aquatic Sciences 38:1128-1140.

Schnute, J. T. 1994. A general framework for developing sequential fisheries models. Canadian Journal of Fisheries and Aquatic Sciences 51:1676-1688.

Self, S. G. and K.-Y. Liang. 1987. Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under nonstandard conditions. Journal of the American Statistical Association 82:605-610.

Shaw, D. J. and A. P. Dobson. 1995. Patterns of macroparasite abundance and aggregation in wildlife populations: A quantitative review. Parasitology 111 Suppl:S111-S127.

Shono, H. 2000. Efficiency of the finite correction of Akaike's Information Criteria. Fisheries Science 66:608-610.

Sibly, R. M., D. Barker, M. C. Denham, J. Hone, and M. Pagel. 2005. On the regulation of populations of mammals, birds, fish, and insects. Science 309:607-610.

Silvertown, J. and M. Dodd. 1999. Evolution of life history in balsam fir (Abies balsamea) in subalpine forests. Proceedings of the Royal Society of London B 266:729-733.

Skaug, H. and D. Fournier. 2006. Automatic approximation of the marginal likelihood in non-Gaussian hierarchical models. Computational Statistics and Data Analysis 51:699-709.

Skellam, J. G. 1951. Random dispersal in theoretical populations. Biometrika 38:196-218. Reprinted in Leslie A. Real and James H. Brown, editors. Foundations of Ecology: Classic Papers with Commentaries, University of Chicago Press, Chicago, 1991.

Sokal, R. R. and F. J. Rohlf. 1995. Biometry, 3d ed. W. H. Freeman, New York.

Solow, A. R. 1998. On fitting a population model in the presence of observation error. Ecology 79:1463-1466.

Spiegelhalter, D. J., N. Best, B. P. Carlin, and A. Van der Linde. 2002. Bayesian measures of model complexity and fit. Journal of the Royal Statistical Society B 64:583-640.

Stefanski, L. A. and J. R. Cook. 1995. Simulation-extrapolation: The measurement error jackknife. Journal of the American Statistical Association 90:1247-1256.

Stephens, P. A., S. W. Buskirk, G. D. Hayward, and C. Martinez del Rio. 2005. Information theory and hypothesis testing: A call for pluralism. Journal of Applied Ecology 42:4-12.

Stram, D. O. and J. W. Lee. 1994. Variance components testing in the longitudinal fixed effects model. Biometrics 50:1171-1177.

Streftaris, G. and G. Gibson. 2004. Bayesian analysis of experimental epidemic of foot-and-mouth disease. Proceedings of the Royal Society of London B 271:1111-1117.

Strong, D. R., A. V. Whipple, A. L. Child, and B. Dennis. 1999. Model selection for a subterranean trophic cascade: Root-feeding caterpillars and entomopathogenic nematodes. Ecology 80:2750-2761.

Swartz, C. 2003. Back-of-the-Envelope Physics. Johns Hopkins University Press, Baltimore, MD.

Szymura, J. M. and N. H. Barton. 1986. Genetic analysis of a hybrid zone between the fire-bellied toads, Bombina bombina and B. variegata, near Cracow in southern Poland. Evolution 40:1141-1159.

Teh, C. 2006. Introduction to Mathematical Modeling of Crop Growth: How the Equations Are Derived and Assembled into a Computer Model. BrownWalker Press, Boca Raton, FL.

Therneau, T. M., P. M. Grambsch, and V. S. Pankratz. 2003. Penalized survival models and frailty. Journal of Computational and Graphical Statistics 12:156-175.

Thomas, L., S. T. Buckland, K. B. Newman, and J. Harwood. 2005. A unified framework for modelling wildlife population dynamics. Australian and New Zealand Journal of Statistics 47:19-34.

Thomas, W. R., M. J. Pomerantz, and M. E. Gilpin. 1980. Chaos, asymmetric growth and group selection for dynamical stability. Ecology 61:1312-1320.

Thompson, D., M. Lonergan, and C. Duck. 2005. Population dynamics of harbour seals Phoca vitulina in England: Monitoring growth and catastrophic declines. Journal of Applied Ecology 42:638-648.

Thomson, J. D., G. Weiblen, B. A. Thomson, S. Alfaro, and P. Legendre. 1996. Untangling multiple factors in spatial distributions: Lilies, gophers, and rocks. Ecology 77: 1698-1715.

Thornley, J. H. 2002. Instantaneous canopy photosynthesis: Analytical expressions for sun and shade leaves based on exponential light decay down the canopy and an acclimated non-rectangular hyperbola for photosynthesis. Annals of Botany 89:451-458.

Tilman, D. 1994. Competition and biodiversity in spatially structured habitats. Ecology 75:2-16.

Tiwari, M., K. A. Bjorndal, A. B. Bolten, and B. M. Bolker. 2005. Intraspecific application of the mid-domain effect model: Spatial and temporal nest distributions of green turtles, Chelonia mydas, at Tortuguero, Costa Rica. Ecology Letters 8:918-924.

——. 2006. Evaluation of density-dependent processes and green turtle Chelonia mydas production at Tortuguero, Costa Rica. Marine Ecological Progress Series 326:283-293.

Tjørve, E. 2003. Shapes and functions of species-area curves: A review of possible models. Journal of Biogeography 30:827-835.

Toms, J. D. and M. L. Lesperance. 2003. Piecewise regression: A tool for identifying ecological thresholds. Ecology 84:2034-2041.

Tracey, J. A., J. Zhu, and K. Crooks. 2005. A set of nonlinear regression models for animal movement in response to a single landscape feature. Journal of Agricultural, Biological, and Environmental Statistics 10:1-18.

Tucci, M. P. 2002. A note on global optimization in adaptive control, econometrics and macroeconomics. Journal of Economic Dynamics and Control 26:1739-1764.

Tufte, E. 2001. The Visual Display of Quantitative Information, 2d ed. Graphics Press, Cheshire, CT.

Tukey, J. W. 1977. Exploratory Data Analysis. Addison-Wesley, Reading, MA.

Turchin, P. 2003. Complex Population Dynamics: A Theoretical/Empirical Synthesis. Princeton University Press, Princeton, NJ.

Tyre, A. J., B. Tenhumberg, S. A. Field, D. Niejalke, K. Parris, and H. P. Possingham. 2003. Improving precision and reducing bias in biological surveys: Estimating false-negative error rates. Ecological Applications 13:1790-1801.

Underwood, A. J. 1996. Experiments in Ecology: Their Logical Design and Interpretation Using Analysis of Variance. Cambridge University Press, Cambridge, England.

van Veen, F. J. F., P. D. van Holland, and H. C. J. Godfray. 2005. Stable coexistence in insect communities due to density- and trait-mediated indirect effects. Ecology 86:1382-1389.

Vandermeer, J. H. and D. E. Goldberg. 2004. Population Ecology: First Principles. Princeton University Press, Princeton, NJ.

Venables, W. N. 1998. Exegeses on linearmodels. 1998 International S-PLUS User Conference. Washington, DC. http://www.stats.ox.ac.uk/pub/MASS3/Exegeses.pdf.

Venables, W. N. and B. D. Ripley. 2002. Modern Applied Statistics with S, 4th ed. Springer, New York.

Verzani, J. 2005. Using R for Introductory Statistics. Chapman and Hall/CRC, Boca Raton, FL.

Vesk, P. A. 2006. Plant size and resprouting ability: Trading tolerance and avoidance of damage? Journal of Ecology 94:1027-1034.

Vigliola, L., P. J. Doherty, M. G. Meekan, D. M. Drown, M. E. Jones, and P. H. Barber. 2007. Genetic identity determines risk of post-settlement mortality of a marine fish. Ecology 88:1263-1277.

Vonesh, J. R. and B. M. Bolker. 2005. Compensatory larval responses shift tradeoffs associated with predator-induced hatching plasticity. Ecology 86:1580-1591.

Walters, C. J. and D. Ludwig. 1981. Effects of measurement errors on the assessment of stock-recruitment relationships. Canadian Journal of Fisheries and Aquatic Sciences 38:704-710.

Wang, D., E. A. Carr, M. R. Palmer, M. W. Berry, and L. J. Gross. 2005. A grid service module for natural-resource managers. IEEE Internet Computing, 9:35-41.

Warton, D. I., I. J. Wright, D. S. Falster, and M. Westoby. 2006. Bivariate line-fitting methods for allometry. Biological Reviews 81:259-291.

Whittingham, M. J., P. A. Stephens, R. B. Bradbury, and R. P. Freckleton. 2006. Why do we still use stepwise modelling in ecology and behaviour? Journal of Animal Ecology 75: 1182-1189.

Wilmshust, J. F., J. M. Fryxell, and P. E. Colucci. 1999. What constrains daily intake in Thomson's gazelles? Ecology 80:2338-2347.

Wilson, J. and C. W. Osenberg. 2002. Experimental and observational patterns of density-dependent settlement and survival in the marine fish Gobiosoma. Oecologia 130:1432-1439.

Wilson, J. A. 2004. Habitat Quality, Competition and Recruitment Processes in Two Marine Gobies. Ph.D. diss. University of Florida, Gainesville.

Wilson, W. 2000. Simulating Ecological and Evolutionary Systems in C. Cambridge University Press, Cambridge, England.

Wintle, B. A. and D. C. Bardos. 2006. Modeling species-habitat relationships with spatially autocorrelated observation data. Ecological Applications 16:1945-1958.

Wood, S. N. 2001. Partially specified ecological models. Ecological Monographs 71:1-25.

——. 2006. Generalized Additive Models: An Introduction with R. Chapman and Hall/CRC, Boca Raton, FL.

Yoccoz, N. G. 1991. Use, overuse and misuse of significance tests in evolutionary biology and ecology. Bulletin of the Ecological Society of America 72:106-111.

Zar, J. H. 1999. Biostatistical Analysis, 4th ed. Prentice Hall, Upper Saddle River, NJ.