Estimating size and composition of biological communities by modeling the occurrence of species

Journal of the American Statistical Association

Volumn 100, Issue 470, 2005, Pages 389-398

  Dorazio, Robert M ^a   Royle, J Andrew ^b  

^a U S GEOLOGICAL SURVEY   (United States)

^b PATUXENT WILDLIFE RESEARCH CENTER   (United States)

Author keywords

Biodiversity; Breeding bird survey; Conservation; Detection heterogeneity; Occurrence heterogeneity; Site occupancy models; Species composition; Species richness

Indexed keywords

EID: 18444403930     PISSN: 01621459     EISSN: None     Source Type: Journal    
DOI: 10.1198/016214505000000015     Document Type: Article

References (46)

1. Agresti, A. (1994), "Simple Capture-Recapture Models Permitting Unequal Catchability and Variable Sampling Effort," Biometrics, 50, 494-500.
2. Barnard, J., McCulloch, R., and Meng, X.-L. (2000), "Modeling Covariance Matrices in Terms of Standard Deviations and Correlations, With Application to Shrinkage," Statistica Sinica, 10, 1281-1311.
3. Basu, S., and Ebrahimi, N. (2001), "Bayesian Capture-Recapture Methods for Error Detection and Estimation of Population Size: Heterogeneity and Dependence," Biometrika, 88, 269-279.
4. Bayley, P. B., and Peterson, J. T. (2001), "An Approach to Estimate Probability of Presence and Richness of Fish Species," Transactions of the American Fisheries Society, 130, 620-633.
5. Boulinier, T., Nichols, J. D., Hines, J. E., Sauer, J. R., Rather, C. H., and Pollock, K. H. (2001), "Forest Fragmentation and Bird Community Dynamics: Inference at Regional Scales," Ecology, 82, 1159-1169.
6. Boulinier, T., Nichols, J. D., Sauer, J. R., Hines, J. E., and Pollock, K. H. (1998), "Estimating Species Richness: The Importance of Heterogeneity in Species Detectability," Ecology, 79, 1018-1028.
7. Bunge, J., and Fitzpatrick, M. (1993), "Estimating the Number of Species: A Review," Journal of the American Statistical Association, 88, 364-373.
8. Burnham, K. P., and Overton, W. S. (1979), "Robust Estimation of Population Size When Capture Probabilities Vary Among Animals," Ecology, 60, 927-936.
9. Cam, E., Nichols, J. D., Hines, J. E., Sauer, J. R., Alpizar-Jara, R., and Flather, C. H. (2002), "Disentangling Sampling and Ecological Explanations Underlying Species-Area Relationships," Ecology, 83, 1118-1130.
10. Cam, E., Nichols, J. D., Sauer, J. R., Hines, J. E., and Flather, C. H. (2000), "Relative Species Richness and Community Completeness: Birds and Urbanization in the Mid-Atlantic States," Ecological Applications, 10, 1196-1210.
11. Carlin, B. P., and Louis, T. A. (2000), Bayes and Empirical Bayes Methods for Data Analysis (2nd ed.), Boca Raton, FL: Chapman & Hall.
12. Colwell, R. K., and Coddington, J. A. (1994), "Estimating Terrestrial Biodiversity Through Extrapolation," Philosophical Transactions of the Royal Society of London, Ser. B, 345, 101-118.
13. Connor, E. F., and McCoy, E. D. (1979), "The Statistics and Biology of the Species-Area Relationship," American Naturalist, 113, 791-833.
14. Coull, B. A., and Agresti, A. (1999), "The Use of Mixed Logit Models to Reflect Heterogeneity in Capture-Recapture Studies," Biometrics, 55, 294-301.
15. Dice, L. R. (1945), "Measures of the Amount of Ecologic Association Between Species," Ecology, 26, 297-302.
16. Doherty, P. F., Jr., Sorci, G., Royle, J. A., Hines, J. E., Nichols, J. D., and Boulinier, T. (2003), "Sexual Selection Affects Local Extinction and Turnover in Bird Communities," Proceedings of the National Academy of Sciences, 100, 5858-5862.
17. Dorazio, R. M., and Royle, J. A. (2003), "Mixture Models for Estimating the Size of a Closed Population When Capture Rates Vary Among Individuals," Biometrics, 59, 351-364.
18. Fienberg, S. E., Johnson, M. S., and Junker, B. W. (1999), "Classical Multilevel and Bayesian Approaches to Population Size Estimation Using Multiple Lists," Journal of the Royal Statistical Society of London, Ser. A, 163, 383-405.
19. Hanski, I. (1992), "Inferences From Ecological Incidence Functions," American Naturalist, 139, 657-662.
20. _ (1994), "A Practical Model of Metapopulation Dynamics," Journal of Animal Ecology, 63, 151-162.
21. Hanski, I., and Gilpin, M. E. (1997), Metapopulation Biology: Ecology, Genetics, and Evolution, New York: Academic Press.
22. James, F. C., McCulloch, C. E., and Wiedenfeld, D. A. (1996), "New Approaches to the Analysis of Population Trends in Land Birds," Ecology, 77, 13-27.
23. Link, W. A. (2003), "Nonidentifiability of Population Size From Capture-Recapture Data With Heterogeneous Detection Probabilities," Biometrics, 59, 1123-1130.
24. Link, W. A., Barker, R. J., Sauer, J. R., and Droege, S. (1994), "Within-Site Variability in Surveys of Wildlife Populations," Ecology, 75, 1097-1108.
25. Link, W. A., and Sauer, J. R. (1997), "Estimation of Population Trajectories From Count Data," Biometrics, 53, 488-497.
26. _ (1998), "Estimating Population Change From Count Data: Application to the North American Breeding Bird Survey," Ecological Applications, 8, 258-268.
27. Liu, Q., and Pierce, D. A. (1994), "A Note on Gauss-Hermite Quadrature," Biometrika, 81, 624-629.
28. MacArthur, R. H., and Wilson, E. O. (1967), The Theory of Island Biogeography, Princeton, NJ: Princeton University Press.
29. MacKenzie, D. I., Nichols, J. D., Lachman, G. B., Droege, S., Royle, J. A., and Langtimm, C. A. (2002), "Estimating Site Occupancy Rates When Detection Probabilities Are Less Than One," Ecology, 83, 2248-2255.
30. Nichols, J. D., Boulinier, T., Hines, J. E., Pollock, K. H., and Sauer, J. R. (1998a), "Estimating Rates of Local Species Extinction, Colonization, and Turnover in Animal Communities," Ecological Applications, 8, 1213-1225.
31. _ (1998b), "Inference Methods for Spatial Variation in Species Richness and Community Composition When Not All Species Are Detected," Conservation Biology, 12, 1390-1398.
32. Nichols, J. D., and Conroy, M. J. (1996), "Estimation of Species Richness," in Measuring and Monitoring Biological Diversity. Standard Methods for Mammals, eds. D. E. Wilson, F. R. Cole, J. D. Nichols, R. Rudran, and M. Foster, Washington, DC: Smithsonian Institution Press, pp. 226-234.
33. Norris, J. L., III, and Pollock, K. H. (1996), "Nonparametric MLE Under Two Closed Capture-Recapture Models With Heterogeneity," Biometrics, 52, 639-649.
34. Pielou, E. C. (1977), Mathematical Ecology, New York: Wiley.
35. Pinheiro, J. C., and Bates, D. M. (1995), "Approximations to the Log-Likelihood Function in the Nonlinear Mixed-Effects Model," Journal of Computational and Graphical Statistics, 4, 12-35.
36. _ (1996), "Unconstrained Parametrizations for Variance-Covariance Matrices," Statistics and Computing, 6, 289-296.
37. Pledger, S. (2000), "Unified Maximum Likelihood Estimates for Closed Capture-Recapture Models Using Mixtures," Biometrics, 56, 434-442.
38. Preston, F. W. (1960), "Time and Space and the Variation of Species," Ecology, 41, 611-627.
39. _ (1962a), "The Canonical Distribution of Commonness and Rarity: Part I," Ecology, 43, 185-215.
40. _ (1962b), "The Canonical Distribution of Commonness and Rarity: Part II," Ecology, 43, 410-432.
41. Robbins, C. S., Bystrak, D., and Geissler, P. H. (1986), "The Breeding Bird Survey: Its First Fifteen Years, 1965-1979," Resource Publication 157, United States Fish and Wildlife Service.
42. Robbins, C. S., Sauer, J. R., Greenberg, R. S., and Droege, S. (1989), "Population Declines in North American Birds That Migrate to the Neotropics," Proceedings of the National Academy of Sciences USA, 86, 7658-7662.
43. Robert, C. P., and Casella, G. (1999), Monte Carlo Statistical Methods, New York: Springer-Verlag.
44. Sanathanan, L. (1972), "Estimating the Size of a Multinomial Population," The Annals of Mathematical Statistics, 43, 142-152.
45. Sauer, J. R., Pendleton, G. W., and Peterjohn, B. G. (1996), "Evaluating Causes of Population Change in North American Insectivorous Songbirds," Conservation Biology, 10, 465-478.
46. Tardella, L. (2002), "A New Bayesian Method for Nonparametric Capture-Recapture Models in Presence of Heterogeneity," Biometrika, 89, 807-817.