What is the animal doing? Tools for exploring behavioural structure in animal movements

Journal of Animal Ecology

Volumn 85, Issue 1, 2016, Pages 69-84

  Gurarie, Eliezer ^a,b   Bracis, Chloe ^b   Delgado, Maria ^c,d   Meckley, Trevor D ^e   Kojola, Ilpo ^f   Wagner, C Michael ^e  

^a University of Maryland   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

^c UNIVERSITY OF HELSINKI   (Finland)

^d UNIVERSITY OF OVIEDO   (Spain)

^e MICHIGAN STATE UNIVERSITY   (United States)

^f FINNISH FOREST RESEARCH INSTITUTE   (Finland)

Author keywords

Behavioural change points; Hidden Markov models; Partitioning; Segmentation; State space models; Telemetry

Indexed keywords

ANIMALIA; CANIS LUPUS; PETROMYZON MARINUS;

ANIMAL; ANIMAL BEHAVIOR; ANIMAL DISPERSAL; BIOLOGICAL MODEL; COMPARATIVE STUDY; ECOLOGY; ETHOLOGY; MOVEMENT (PHYSIOLOGY); PETROMYZON; PHYSIOLOGY; PROCEDURES; WOLF;

ANIMAL DISTRIBUTION; ANIMALS; ECOLOGY; ETHOLOGY; HOMING BEHAVIOR; MODELS, BIOLOGICAL; MOVEMENT; PETROMYZON; WOLVES;

EID: 84937683345     PISSN: 00218790     EISSN: 13652656     Source Type: Journal    
DOI: 10.1111/1365-2656.12379     Document Type: Article

References (59)

1. Barraquand, F. & Benhamou, S. (2008) Animal movements in heterogeneous landscapes: identifying profitable places and homogeneous movement bouts. Ecology, 89, 3336-3348.
2. Benaglia, T., Chauveau, D., Hunter, D.R. & Young, D. (2009) mixtools: an R Package for Analyzing Finite Mixture Models. Journal of Statistical Software, 32, 1-29.
3. Benhamou, S. (2004) How to reliably estimate the tortuosity of an animal's path: straightness, sinuosity, or fractal dimenion? Journal of Theoretical Biology, 229, 209-220.
4. Benhamou, S. (2006) Detecting an orientation component in animal paths when the preferred direction is individual-dependent. Ecology, 87, 518-528.
5. Beyer, H., Morales, J., Murray, D. & Fortin, M.J. (2013) The effectiveness of Bayesian state-space models for estimating behavioural states from movement paths. Methods in Ecology and Evolution, 4, 433-441.
6. Blackwell, P. (1997) Random diffusion models for animal movement. Ecological Modelling, 100, 87-102.
7. Block, B., Dewar, H., Blackwell, S., Williams, T., Prince, E., Farwell, C. et al. (2001) Migratory movements, depth preferences, and thermal biology of Atlantic bluefin tuna. Science, 293, 1310-1314.
8. Börger, L. & Fryxell, J.M. (2012) Quantifying individual differences in dispersal using net squared displacement. Dispersal and Spatial Evolutionary Ecology (eds J. Clobert, M. Baguette, T. Benton & J. Bullock ), Oxford University Press, Oxford, UK.
9. Bovet, P. & Benhamou, S. (1988) Spatial analysis of animal's movements using a correlated random walk model. Journal of Theoretical Biology, 131, 419-433.
10. Boyce, M., Pitt, J., Northrup, J., Morehouse, A., Knopff, K., Cristescu, B. et al. (2010) Temporal autocorrelation functions for movement rates from global positioning system radiotelemetry data. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 365, 2213-2219.
11. Breed, G.A., Costa, D., Jonsen, I., Robinson, P. & Mills-Flemming, J. (2012) State-space methods for more completely capturing behavioral dynamics from animal tracks. Ecological Modelling, 235, 49-58.
12. Cagnacci, F., Boitani, L., Powell, R.A. & Boyce, M.S. (2010) Animal ecology meets GPS-based radiotelemetry: a perfect storm of opportunities and challenges. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 365, 2157-2162.
13. Calenge, C. (2006) The package adehabitat for the R software: tool for the analysis of space and habitat use by animals. Ecological Modelling, 197, 1035.
14. Delgado, M.d.M., Penteriani, V., Revilla, E. & Nams, V.O. (2010) The effect of phenotypic traits and external cues on natal dispersal movements. Journal of Animal Ecology, 79, 620-632.
15. Delgado, M., Penteriani, V., Morales, J., Gurarie, E. & Ovaskainen, O. (2014) A statistical framework for inferring the influence of conspecifics on movement behaviour. Methods in Ecology and Evolution, 5, 183-189.
16. Fagan, W., Lewis, M., Auger-Méthé, M., Avgar, T., Benhamou, S., Breed, G. et al. (2013) Spatial memory and animal movement. Ecology Letters, 16, 1316-1329.
17. Fauchald, P. & Tveraa, T. (2003) Using first-passage time in the analysis of area-restricted search and habitat selection. Ecology, 84, 282-288.
18. Fleming, C.H., Calabrese, J.M., Mueller, T., Olson, K.A., Leimgruber, P. & Fagan, W.F. (2014) Non-Markovian maximum likelihood estimation of autocorrelated movement processes. Methods in Ecology and Evolution, 5, 462-472.
19. Forester, J.D., Ives, A.R., Turner, M.G., Anderson, D. P., Fortin, D., Beyer, H.L. et al. (2007) State-space models link elk movement patterns to landscape characteristics in Yellowstone National Park. Ecological Monographs, 77, 285-299.
20. Fritz, H., Said, S. & Weimerskirch, H. (2003) Scale-dependent hierarchical adjustments of movement patterns in a long-range foraging seabird. Proceedings of the Royal Society of London. Series B: Biological Sciences, 270, 1143-1148.
21. Guéguen, L. (2001) Segmentation by maximal predictive partitioning according to composition biases. Computational Biology, pp. 32-44. Springer, Berlin.
22. Guéguen, L. (2009) Computing the likelihood of sequence segmentation under Markov modelling. arXiv preprint arXiv:0911.3070.
23. Gurarie, E. (2013) bcpa: Behavioral Change Point Analysis of Animal Movement (R package version 1.0).
24. Gurarie, E. & Ovaskainen, O. (2011) Characteristic spatial and temporal scales unify models of animal movement. The American Naturalist, 178, 113-123.
25. Gurarie, E., Andrews, R.D. & Laidre, K.L. (2009) A novel method for identifying behavioural changes in animal movement data. Ecology Letters, 12, 395-408.
26. Gurarie, E., Suutarinen, J., Kojola, I. & Ovaskainen, O. (2011) Summer movements, predation and habitat use of wolves in human modified boreal forests. Oecologia, 165, 891-903.
27. Hanski, I. (1998) Metapopulation dynamics. Nature, 396, 41-49.
28. Johnson, D.S., London, J., Lea, M.A. & Durban, J. (2008) Continuous-time correlated random walk model for animal telemetry data. Ecology, 89, 1208-1215.
29. Jonsen, I.D., Myers, R.A. & Flemming, J.M. (2005) Robust state-space modeling of animal movement data. Ecology, 86, 2874-2880.
30. Jonsen, I., Basson, M., Bestley, S., Bravington, M.V., Patterson, T.A., Pedersen, M.W. et al. (2013) State-space models for bio-loggers: a methodological roadmap. Deep-Sea Research II, 88, 34-46.
31. Kareiva, P.M. & Shigesada, N. (1983) Analyzing insect movement as a correlated random walk. Oecologia, 56, 234-238.
32. Kareiva, P., Mullen, A. & Southwood, R. (1990) Population dynamics in spatially complex environments: theory and data [and discussion]. Philosophical Transactions of the Royal Society B: Biological Sciences, 330, 175-190.
33. Keeling, M. & Grenfell, B. (1997) Disease extinction and community size: modeling the persistence of measles. Science, 275, 65-67.
34. Kojola, I., Aspi, J., Hakala, A., Heikkinen, S., Ilmoni, C. & Ronkainen, S. (2006) Dispersal in an expanding wolf population in Finland. Journal of Mammalogy, 87, 281-286.
35. Kranstauber, B., Kays, R., LaPoint, S.D., Wikelski, M. & Safi, K. (2012) A dynamic Brownian bridge movement model to estimate utilization distributions for heterogeneous animal movement. Journal of Animal Ecology, 81, 738-746.
36. Laidre, K., Heide-Jørgensen, M., Logsdon, M., Hobbs, R., Dietz, R. & VanBlaricom, G. (2004) Fractal analysis of narwhal space use patterns. Applied Entomology and Zoology, 107, 3-11.
37. Langrock, R., King, R., Matthiopoulos, J., Thomas, L., Fortin, D. & Morales, J.M. (2012) Flexible and practical modeling of animal telemetry data: hidden Markov models and extensions. Ecology, 93, 2336-2342.
38. Lavielle, M. (2005) Using penalized contrasts for the change-point problem. Analog Integrated Circuits and Signal Processing, 85, 1501-1510.
39. McClintock, B.T., King, R., Thomas, L., Matthiopoulos, J., McConnell, B.J. & Morales, J.M. (2012) A general discrete-time modeling framework for animal movement using multistate random walks. Ecological Monographs, 82, 335-349.
40. McClintock, B., Russell, D., Matthiopoulos, J. & King, R. (2013) Combining individual animal movement and ancillary biotelemetry data to investigate population-level activity budgets. Ecology, 94, 838-849.
41. McLachlan, G. & Peel, D. (2000) Finite Mixture Models. John Wiley and Sons, Inc., New York.
42. Meckley, T., Wagner, C., Gurarie, E. & Tierney, K. (2014a) Sea lamprey (Petromyzon marinus) movements and odor-mediated search behavior near coastlines during the reproductive migration. Canadian Journal of Fisheries and Aquatic Sciences, 71, 533-544.
43. Meckley, T.D., Holbrook, C.M., Wagner, C.M. & Binder, T.R. (2014b) An approach for filtering hyperbolically positioned underwater acoustic telemetry data with position precision estimates. Animal Biotelemetry, 2, 7.
44. Moorcroft, P.R., Lewis, M.A. & Crabtree, R.L. (1999) Home range analysis using a mechanistic home range model. Ecology, 80, 1656-1665.
45. van Moorter, B., Visscher, D.R., Jerde, C.L., Frair, J.L. & Merrill, E.H. (2010) Identifying movement states from location data using cluster analysis. Journal of Wildlife Management, 74, 588-594.
46. Morales, J.M., Haydon, D.T., Frair, J., Holsinger, K.E. & Fryxell, J.M. (2004) Extracting more out of relocation data: building movement models as mixtures of random walks. Ecology, 85, 2436-2445.
47. Morales, J.M., Moorcroft, P.R., Matthiopoulos, J., Frair, J.L., Kie, J.G., Powell, R.A. et al. (2010) Building the bridge between animal movement and population dynamics. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 365, 2289-2301.
48. Morgan, E.R., Milner-Gulland, E., Torgerson, P.R. & Medley, G.F. (2004) Ruminating on complexity: macroparasites of wildlife and livestock. Trends in Ecology & Evolution, 19, 181-188.
49. Nams, V.O. (2013) Sampling animal movement paths causes turn autocorrelation. Acta Biotheoretica, 61, 269-284.
50. Nams, V.O. & Bourgeois, M. (2004) Fractal analysis measures habitat use at different spatial scales: an example with American marten. Canadian Journal of Zoology, 82, 1738-1747.
51. Patterson, T., Thomas, L., Wilcox, C., Ovaskainen, O. & Matthiopoulos, J. (2008) State-space models of individual animal movement. Trends in Ecology & Evolution, 23, 87-94.
52. Plummer, M. (2013) rjags: Bayesian graphical models using MCMC. R package version 3-10. Available from: http://CRAN.R-project.org/package=rjags.
53. Plummer, M., Best, N., Cowles, K. & Vines, K. (2006) CODA: Convergence Diagnosis and Output Analysis for MCMC. R News, 6, 7-11.
54. Polansky, L., Wittemyer, G., Cross, P.C., Tambling, C.J. & Getz, W.M. (2010) From moonlight to movement and synchronized randomness: fourier and wavelet analyses of animal location time series data. Ecology, 91, 1506-1518.
55. Su, Y.S. & Yajima, M. (2012) R2jags: A Package for Running jags from R. R package version 0.03-08. Available from: http://CRAN.R-project.org/package=R2jags.
56. Tremblay, Y., Roberts, A.J. & Costa, D.P. (2007) Fractal landscape method: an alternative approach to measuring area-restricted searching behavior. Indian Journal of Experimental Biology, 210, 935-945.
57. Turchin, P. (1991) Translating foraging movements in heterogeneous environments into the spatial distribution of foragers. Ecology, 72, 1253-1266.
58. Turchin, P. (1998) Quantitative Analysis of Movement: Measuring and Modeling Population Redistribution in Animals and Plants. Sinauer, Sunderland, MA.
59. Vrieze, L., Bergstedt, R. & Sorensen, P. (2011) Olfactory-mediated stream-finding behavior of migratory adult sea lamprey (Petromyzon marinus). Canadian Journal of Fisheries and Aquatic Sciences, 68, 523-533.