Hierarchical Bayes estimation of species richness and occupancy in spatially replicated surveys

Journal of Applied Ecology

Volumn 45, Issue 2, 2008, Pages 589-598

  Kery M ^a   Royle, J A ^b  

^a SWISS ORNITHOLOGICAL INSTITUTE   (Switzerland)

^b PATUXENT WILDLIFE RESEARCH CENTER   (United States)

Author keywords

Biodiversity; Breeding bird survey; MCMC; Monitoring; Multilevel; Multisite estimation; WinBUGS

Indexed keywords

BAYESIAN ANALYSIS; BIODIVERSITY; BIOGEOGRAPHY; BIVALVE; BREEDING POPULATION; COMMUNITY STRUCTURE; COVARIANCE ANALYSIS; ENVIRONMENTAL MONITORING; SPECIES RICHNESS;

AVES;

EID: 40949153521     PISSN: 00218901     EISSN: 13652664     Source Type: Journal    
DOI: 10.1111/j.1365-2664.2007.01441.x     Document Type: Article

References (49)

1. Bailey, L.L., Hines, J.E., Nichols, J.D. MacKenzie, D.I. (2007) Sampling design trade-offs in occupancy studies with imperfect detection: examples and software. Ecological Applications, 17, 281 290.
2. Boulinier, T., Nichols, J.D., Sauer, J.R., Hines, J.E. Pollock, K.H. (1998a) Estimating species richness: the importance of heterogeneity in species detectability. Ecology, 79, 1018 1028.
3. Boulinier, T., Nichols, J.D., Hines, J.E., Sauer, J.R., Flather, C.H. Pollock, K.H. (1998b) Higher temporal variability of forest breeding bird communities in fragmented landscapes. Proceedings of the National Academy of Sciences, USA, 95, 7497 7501.
4. Boulinier, T., Nichols, J.D., Hines, J.E., Sauer, J.R., Flather, C.H. Pollock, K.H. (2001) Forest fragmentation and bird community dynamics: inference at regional scales. Ecology, 82, 1159 1169.
5. Brooks, S.P. (2003) Bayesian computation: a statistical revolution. Philosophical Transactions of the Royal Society A, 361, 2681 2697.
6. Burnham, K.P. Overton, W.S. (1979) Robust estimation of population size when capture probabilities vary among animals. Ecology, 60, 927 936.
7. Cam, E., Nichols, J.D., Hines, J.E., Sauer, J.R., Alpizar-Jara, R. Flather, C.H. (2002) Disentangling sampling and ecological explanations underlying species-area relationships. Ecology, 83, 1118 1130.
8. Chao, A. (2005) Species richness estimation. Encyclopedia of Statistical Sciences (eds N. Balakrishnan, C.B. Read B. Vidakovic), pp. 7909 7916. Wiley, New York.
9. Conn, P.B., Arthur, A.D., Bailey, L.L. Singleton, G.R. (2006) Estimating the abundance of mouse populations of known size: promises and pitfalls of new methods. Ecological Applications, 16, 829 837.
10. Doherty, Jr., P.F., Sorci, G., Royle, J.A., Hines, J.E., Nichols, J.D. Boulinier, T. (2003) Sexual selection affects local extinction and turnover in bird communities. Proceedings of the National Academy of Sciences, USA, 100, 5858 5862.
11. Dorazio, R.M. Royle, J.A. (2005) Estimating size and composition of biological communities by modeling the occurrence of species. Journal of the American Statistical Association, 100, 389 398.
12. Dorazio, R.M., Royle, J.A., Söderström, B. Glimskär, A. (2006) Estimating species richness and accumulation by modeling species occurrence and detectability. Ecology, 87, 842 854.
13. Ellison, A.M. (2004) Bayesian inference in ecology. Ecology Letters, 7, 509 520.
14. Gelfand, A.E., Schmidt, A.E., Wu, S., Silander, Jr., J.A., Latimer, A. Rebelo, A.G. (2005) Modelling species diversity through species level hierarchical modelling. Applied Statistics, 54, 1 20.
15. Gelman, A. Rubin, D.B. (1992) Inference from iterative simulation using multiple sequences. Statistical Science, 7, 457 511.
16. Gotelli, N.J. (2000) Null-model analysis of species co-occurrence patterns. Ecology, 81, 2606 2621.
17. Hines, J.E., Boulinier, T., Nichols, J.D., Sauer, J.R. Pollock, K.H. (1999) comdyn: software to study the dynamics of animal communities using a capture-recapture approach. Bird Study, 46, S209 S217.
18. Howard, P.C., Davenport, T.R.B., Kigenyi, F.W. et al 2000) Protected area planning in the tropics: Uganda's national system of forest nature reserves. Conservation Biology, 14, 858 875.
19. Jetz, W. Rahbek, C. (2002) Geographic range size and determinants of avian species richness. Science, 297, 1548 1551.
20. Karanth, K.K., Nichols, J.D., Sauer, J.R. Hines, J.E. (2006) Comparative dynamics of avian communities across edges and interiors of North American ecoregions. Journal of Biogeography, 33, 674 682.
21. Kéry, M. (2002) Inferring the absence of a species - a case study of snakes. Journal of Wildlife Management, 66, 330 338.
22. Kéry, M. Plattner, M. (2007) Species richness estimation and determinants of species detectability in butterfly monitoring programs. Ecological Entomology, 32, 53 61.
23. Kéry, M. Royle, J.A. (2008) Inference about species richness and community structure using species-specific occupancy models in the national Swiss breeding bird survey MHB. Environmental and Ecological Statistics, in press.
24. Kéry, M. Schmid, H. (2006) Estimating species richness: calibrating a large avian monitoring programme. Journal of Applied Ecology, 43, 101 110.
25. Kéry, M., Royle, J.A. Schmid, H. (2005) Modeling avian abundance from replicated counts using binomial mixture models. Ecological Applications, 15, 1450 1461.
26. Lekve, K., Boulinier, T., Stenseth, N.C. et al 2002) Spatio-temporal dynamics of species richness in coastal fish communities. Proceedings of the Royal Society of London, Series B - Biological Sciences, 269, 1781 1789.
27. Link, W.A. (1999) Modeling pattern in collections of parameters. Journal of Wildlife Management, 63, 1017 1027.
28. Link, W.A. (2003) Nonidentifiability of population size from capture-recapture data with heterogeneous detection probabilities. Biometrics, 59, 1123 1130.
29. Link, W.A., Cam, E., Nichols, J.D. Cooch, E.D. (2002) Of BUGS and birds: Markov chain Monte Carlo for hierarchical modeling in wildlife research. Journal of Wildlife Management, 66, 277 291.
30. Longino, J.T., Coddington, J. Colwell, R.K. (2002) The ant fauna of a tropical rain forest: estimating species richness three different ways. Ecology, 83, 689 702.
31. MacKenzie, D.I. Royle, J.A. (2005) Designing efficient occupancy studies: general advice and tips on allocation of survey effort. Journal of Applied Ecology, 42, 1105 1114.
32. MacKenzie, D.I., Nichols, J.D., Royle, J.A., Pollock, K.H., Bailey, L.L. Hines, J.E. (2006) Occupancy Estimation and Modeling - Inferring Patterns and Dynamics of Species Occurrence. Elsevier, San Diego, CA, USA.
33. Mao, C.X. Colwell, R.K. (2005) Estimation of species richness: mixture models, the role of rare species, and inferential challenges. Ecology, 86, 1143 1153.
34. McCoy, E.D. Heck, Jr., K.L. (1987) Some observations on the use of taxonomic similarity in large-scale biogeography. Journal of Biogeography, 14, 79 87.
35. Nichols, J.D., Boulinier, T., Hines, J.E., Pollock, K.H. Sauer, J.R. (1998a) Inference methods for spatial variation in species richness and community composition when not all species are detected. Conservation Biology, 12, 1390 1398.
36. Nichols, J.D., Boulinier, T., Hines, J.E., Pollock, K.H. Sauer, J.R. (1998b) Estimating rates of local species extinction, colonization, and turnover in animal communities. Ecological Applications, 8, 1213 1225.
37. Novotny, V. Basset, Y. (2000) Rare species in communities of tropical insect herbivores: pondering the mystery of singletons. Oikos, 89, 564 572.
38. O'Hara, R.B. (2005) Species richness estimators: how many species can dance on the head of a pin? Journal of Animal Ecology, 74, 375 386.
39. Otis, D.L., Burnham, K.P., White, G.C. Anderson, D.R. (1978) Statistical inference for capture data on closed animal populations. Wildlife Monographs, 62, 1 135.
40. Purvis, A. Hector, A. (2000) Getting the measure of biodiversity. Nature, 405, 212 219.
41. Royle, J.A. Kéry, M. (2007) A Bayesian state-space formulation of dynamic occupancy models. Ecology, 88, 1813 1823.
42. Royle, J.A. Link, W.A. (2006) Generalized site occupancy models allowing for false positive and false negative errors. Ecology, 87, 835 841.
43. Royle, J.A. Nichols, J.D. (2003) Estimating abundance from repeated presence-absence data or point counts. Ecology, 84, 777 790.
44. Royle, J.A., Dorazio, R.M. Link, W.A. (2007) Analysis of multinomial models with unknown index using data augmentation. Journal of Computational and Graphical Statistics, 16, 67 85.
45. Schmid, H., Zbinden, N. Keller, V. (2004) Überwachung der Bestandsentwicklung Häufiger Brutvögel in der Schweiz. Swiss. Ornithological Institute, Sempach, Switzerland.
46. Spiegelhalter, D., Thomas, A., Best, N. Lunn, D. (2003) WinBUGS version 1.4, User Manual. MRC Biostatistics Unit, Cambridge, UK.
47. Weber, D., Hintermann, U. Zangger, A. (2004) Scale and trends in species richness: considerations for monitoring biological diversity for political purposes. Global Ecology and Biogeography, 13, 97 104.
48. Williams, B.K., Nichols, J.D. Conroy, M.J. (2002) Analysis and Management of Animal Populations. Academic Press, San Diego, CA, USA.
49. Yoccoz, N.G., Nichols, J.D. Boulinier, T. (2001) Monitoring of biological diversity in space and time. Trends in Ecology and Evolution, 16, 446 445.