Spatiotemporal hierarchical modelling of species richness and occupancy using camera trap data

Journal of Applied Ecology

Volumn 52, Issue 2, 2015, Pages 413-421

  Tobler, Mathias W ^a   Zúñiga Hartley, Alfonso ^b   Carrillo Percastegui, Samia E ^c   Powell, George V N ^c  

^a INSTITUTE FOR CONSERVATION RESEARCH   (United States)

^b World Wildlife Fund Peru   (Peru)

^c Conservation Science Program ^*  (United States)

Author keywords

Amazon; Bayesian model; Inventory; Madre de Dios; Monitoring; Multi species occupancy model; Peru; Terrestrial mammals

Indexed keywords

DATA SET; HABITAT SELECTION; HIERARCHICAL SYSTEM; IMAGE ANALYSIS; MAMMAL; MODEL TEST; SPATIOTEMPORAL ANALYSIS; SPECIES INVENTORY; SPECIES RICHNESS;

BRAZIL; PERU;

BERTHOLLETIA EXCELSA; MAMMALIA; VERTEBRATA;

EID: 84924629684     PISSN: 00218901     EISSN: 13652664     Source Type: Journal    
DOI: 10.1111/1365-2664.12399     Document Type: Article

References (43)

1. Ahumada, J.A., Hurtado, J. & Lizcano, D. (2013) Monitoring the status and trends of tropical forest terrestrial vertebrate communities from camera trap data: a tool for conservation. PLoS One, 8, e73707.
2. Ahumada, J.A., Silva, C.E.F., Gajapersad, K., Hallam, C., Hurtado, J., Martin, E. et al. (2011) Community structure and diversity of tropical forest mammals: data from a global camera trap network. Philosophical Transactions of the Royal Society B: Biological Sciences, 366, 2703-2711.
3. Azlan, J.M. (2006) Mammal diversity and conservation in a secondary forest in Peninsular Malaysia. Biodiversity and Conservation, 15, 1013-1025.
4. Burton, A.C., Sam, M.K., Balangtaa, C. & Brashares, J.S. (2012) Hierarchical multi-species modeling of carnivore responses to hunting, habitat and prey in a West African protected area. PLoS One, 7, e38007.
5. DeWan, A.A. & Zipkin, E.F. (2010) An integrated sampling and analysis approach for improved biodiversity monitoring. Environmental Management, 45, 1223-1230.
6. 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.
7. Dorazio, R.M., Royle, J.A., Soderstrom, B. & Glimskar, A. (2006) Estimating species richness and accumulation by modeling species occurrence and detectability. Ecology, 87, 842-854.
8. Dorazio, R.M., Kéry, M., Royle, J.A. & Plattner, M. (2010) Models for inference in dynamic metacommunity systems. Ecology, 91, 2466-2475.
9. Efford, M.G. (2013) secr: Spatially explicit capture-recapture models. R package version 2.6.1.
10. Efford, M.G. & Dawson, D.K. (2012) Occupancy in continuous habitat. Ecosphere, 3, art32.
11. Fiske, I. & Chandler, R. (2011) Unmarked: an R package for fitting hierarchical models of wildlife occurrence and abundance. Journal of Statistical Software, 43, 1-23.
12. Gelman, A. (2006) Prior distributions for variance parameters in hierarchical models. Bayesian Analysis, 1, 515-534.
13. Gelman, A. & Rubin, D.B. (1992) Inference from iterative simulation using multiple sequences. Statistical Science, 7, 457-472.
14. Gotelli, N.J. & Colwell, R.K. (2001) Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness. Ecology Letters, 4, 379-391.
15. Harmsen, B.J., Foster, R.J., Silver, S., Ostro, L. & Doncaster, C.P. (2010) Differential use of trails by forest mammals and the implications for camera-trap studies: a case study from Belize. Biotropica, 42, 126-133.
16. Kéry, M. (2011) Species richness and community dynamics: a conceptual framework. Camera Traps in Animal Ecology: Methods and Analyses (eds A.F. O'Connell, J.D. Nichol & K.U. Karanth ), pp. 207-231. Springer, New York.
17. Kéry, M. & Schaub, M. (2012) Bayesian Population Analysis Using WinBUGS a Hierarchical Perspective. Elsevier, Amsterdam.
18. Kéry, M., Royle, J.A., Plattner, M. & Dorazio, R.M. (2009) Species richness and occupancy estimation in communities subject to temporary emigration. Ecology, 90, 1279-1290.
19. Kitamura, S., Thong-Aree, S., Madsri, S. & Poonswad, P. (2010) Mammal diversity and conservation in a small isolated forest of Southern Thailand. Raffles Bulletin of Zoology, 58, 145-156.
20. Mackenzie, D.I. & Royle, J.A. (2005) Designing occupancy studies: general advice and allocating survey effort. Journal of Applied Ecology, 42, 1105-1114.
21. 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, Amsterdam.
22. McCallum, J. (2013) Changing use of camera traps in mammalian field research: habitats, taxa and study types. Mammal Review, 43, 196-206.
23. Nichols, J.D., Karanth, K.U. & O'Connell, A.F. (2011) Science, conservation, and camera traps. Camera Traps in Animal Ecology: Methods and Analyses (eds A.F. O'Connell, J.D. Nichol & K.U. Karanth ), pp. 45-56. Springer, New York.
24. Nichols, J.D., Boulinier, T., Hines, J.E., Pollock, K.H. & Sauer, J.R. (1998) Inference methods for spatial variation in species richness and community composition when not all species are detected. Conservation Biology, 12, 1390-1398.
25. O'Brien, T.G., Kinnaird, M.F. & Wibisono, H.T. (2011) Estimation of species richness of large vertebrates using camera traps: an example from an Indonesian rainforest. Camera Traps in Animal Ecology: Methods and Analyses (eds A.F. O'Connell, J.D. Nichol & K.U. Karanth ), pp. 233-252. Springer, New York.
26. O'Brien, T.G., Baillie, J.E.M., Krueger, L. & Cuke, M. (2010) The Wildlife Picture Index: monitoring top trophic levels. Animal Conservation, 13, 335-343.
27. Peres, C.A. (1996) Population status of white-lipped Tayassu pecari and collared peccaries T. tajacu in hunted and unhunted Amazonian forests. Biological Conservation, 77, 115-123.
28. Peres, C.A. & Palacios, E. (2007) Basin-wide effects of game harvest on vertebrate population densities in Amazonian forests: implications for animal-mediated seed dispersal. Biotropica, 39, 304-315.
29. Plummer, M. (2003) JAGS: A program for analysis of Bayesian graphical models using Gibbs sampling. Proceedings of the 3rd International Workshop on Distributed Statistical Computing. Vienna, Austria.
30. Rovero, F. & De Luca, D.W. (2007) Checklist of mammals of the Udzungwa mountains of Tanzania. Mammalia, 71, 47-55.
31. Royle, J.A. (2006) Site occupancy models with heterogeneous detection probabilities. Biometrics, 62, 97-102.
32. Royle, J.A. & Nichols, J.D. (2003) Estimating abundance from repeated presence-absence data or point counts. Ecology, 84, 777-790.
33. Royle, J.A., Chandler, R.B., Sollmann, R. & Gardner, B. (2013) Spatial Capture-Recapture. Academic Press, Waltham, MA, USA.
34. Russell, R.E., Royle, J.A., Saab, V.A., Lehmkuhl, J.F., Block, W.M. & Sauer, J.R. (2009) Modeling the effects of environmental disturbance on wildlife communities: avian responses to prescribed fire. Ecological Applications, 19, 1253-1263.
35. Schaub, M. & Kéry, M. (2012) Combining information in hierarchical models improves inferences in population ecology and demographic population analyses. Animal Conservation, 15, 125-126.
36. Tobler, M.W., Carrillo-Percastegui, S.E. & Powell, G. (2009) Habitat use, activity patterns and use of mineral licks by five species of ungulate in south-eastern Peru. Journal of Tropical Ecology, 25, 261-270.
37. Tobler, M.W., Carrillo-Percastegui, S.E., Pitman, R.L., Mares, R. & Powell, G. (2008) An evaluation of camera traps for inventorying large- and medium-sized terrestrial rainforest mammals. Animal Conservation, 11, 169-178.
38. Tobler, M.W., Carrillo-Percastegui, S.E., Zúñiga Hartley, A. & Powell, G.V.N. (2013) High jaguar densities and large population sizes in the core habitat of the southwestern Amazon. Biological Conservation, 159, 375-381.
39. White, G.C., Anderson, D.R., Burnham, K.P. & Otis, D.L. (1982) Capture-Recapture and Removal Methods for Sampling Closed Populations. Los Alamos National Laboratory, Los Alamos, N.M., Springfield, VA, USA.
40. Yamaura, Y., Andrew Royle, J., Kuboi, K., Tada, T., Ikeno, S. & Makino, S.i. (2011) Modelling community dynamics based on species-level abundance models from detection/nondetection data. Journal of Applied Ecology, 48, 67-75.
41. Zipkin, E.F., DeWan, A. & Royle, A.J. (2009) Impacts of forest fragmentation on species richness: a hierarchical approach to community modelling. Journal of Applied Ecology, 46, 815-822.
42. Zipkin, E.F., Grant, E.H.C. & Fagan, W.F. (2012) Evaluating the predictive abilities of community occupancy models using AUC while accounting for imperfect detection. Ecological Applications, 22, 1962-1972.
43. Zipkin, E.F., Andrew Royle, J., Dawson, D.K. & Bates, S. (2010) Multi-species occurrence models to evaluate the effects of conservation and management actions. Biological Conservation, 143, 479-484.