Fitting complex ecological point process models with integrated nested Laplace approximation

Methods in Ecology and Evolution

Volumn 4, Issue 4, 2013, Pages 305-315

  Illian, Janine B ^a   Martino, Sara ^b   Sørbye, Sigrunn H ^c   Gallego Fernández, Juan B ^d   Zunzunegui, María ^d   Esquivias, M Paz ^d   Travis, Justin M J ^d  

^a UNIVERSITY OF ST ANDREWS   (United Kingdom)

^b NORWEGIAN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Norway)

^c UNIVERSITY OF TROMSØ   (Norway)

^d UNIVERSITY OF ABERDEEN   (United Kingdom)

Author keywords

Log Gaussian Cox processes; Marked point patterns; Spatial modelling

Indexed keywords

THYMUS CARNOSUS;

EID: 84875769838     PISSN: None     EISSN: 2041210X     Source Type: Journal    
DOI: 10.1111/2041-210x.12017     Document Type: Article

References (50)

1. Aarts, G., Fieberg, J. & Matthiopoulos, J. (2012) Comparative interpretation of count, presence-absence and point methods for species distribution models. Methods in Ecology and Evolution, 3, 177-187.
2. Alés, E.E., Sánchez Gullón, E. & Peña, J. (2003) Consideraciones sobre la categoría de amenaza para Thymus carnosus en el suroeste de España. Conservacion Vegetal. Boletin de la comision de flora del comite espanol de la U.I.C.N., 8, 9-10.
3. Baddeley, A.J. & Turner, R. (2005) Spatstat: an R package for analyzing spatial point patterns. Journal of Statistical Software, 12, 1-42.
4. Beale, C.M., Lennon, J.J., Yearsley, J.M., Brewer, M.J. & Elston, D.A. (2010) Regression analysis of spatial data. Ecology Letters, 13, 246-264.
5. Brooks, S.P., King, R. & Morgan, B.J.T. (2004) A Bayesian approach to combining animal abundance and demographic data. Animal Biodiversity and Conservation, 27, 515-529.
6. Brown, C., Law, R., Illian, J.B. & Burslem, D. (2011) Linking ecological processes with spatial and non-spatial patterns in plant communities. Journal of Ecology, 99, 1402-1414.
7. Cabezudo, B., Talavera, S., Blanca, G., Salazar, C., Cueto, M., Valdés, B., Hernández-Bermejo, E., Herrera, C.M., Rodríguez-Hiraldo, C. & Navas, D. (2005) Lista Roja de la Flora Vascular de Andalucía. Consejería de Medio Ambiente, Junta de Andalucía, Seville.
8. Collins, D. & Bras, R. (2007) Plant rooting strategies in water-limited ecosystems. Water Resources Research, 43, W06407.
9. Cornulier, T. & Bretagnolle, V. (2006) Assessing the influence of environmental heterogeneity on bird spacing patterns: a case study with two raptors. Ecography, 29, 240-250.
10. Dawson, T. & Pate, J. (1996) Seasonal water uptake and movement in root systems of Australian phraeatophytic plants of dimorphic root morphology: a stable isotope investigation. Oecologia, 107, 13-20.
11. Diggle, P. (2003) Statistical Analysis of Spatial Point Patterns, 2nd edn. Hodder Arnold, London.
12. Diggle, P. (2007) Spatio-temporal point processes: methods and applications. Statistical Methods for Spatio-temporal Systems (eds B. Finkenstädt, L. Held & V. Isham), pp. 1-45. Chapman & Hall/CRC Press, Boca Raton, Florida, USA.
13. Diggle, P., Menezes, R. & Su, T. (2010) Geostatistical inference under preferential sampling (with discussion). Journal of the Royal Statistical Society Series C, 59, 191-232.
14. Diggle, P.J. & Ribeiro, P.J. (2007) Model-Based Geostatistics (Springer Series in Statistics). Springer, New York.
15. Gallego-Fernández, J., Muñoz Vallés, S. & Dellafiore, C. (2006) Flora and Vegetation on Nueva Umbria Spit (Lepe, Huelva). Lepe Council, Lepe.
16. Ho, L.P. & Stoyan, D. (2008) Modelling marked point patterns by intensity-marked Cox processes. Statistical Probability Letters, 78, 1194-1199.
17. Illian, J.B., Penttinen, A., Stoyan, D. & Stoyan, H. (2008) Analysis and Modelling of Spatial Point Patterns. Wiley, Chichester.
18. Illian, J.B. & Rue, H. (2010) A toolbox for fitting complex spatial point process models using integrated Laplace transformation (INLA). Technical Report, Trondheim University.
19. Illian, J.B., Sørbye, S.H. & Rue, H. (2012) A toolbox for fitting complex spatial point process models using integrated nested Laplace approximation (INLA). Annals of Applied Statistics, 6, 1499-1530.
20. Illian, J.B., Sørbye, S.H., Rue, H. & Hendrichsen, D.K. (2012) Fitting a log Gaussian Cox process with temporally varying effects - a case study. Journal of Environmental Statistics, 3, 1-25.
21. Jenerette, G., Barron-Gafford, G., Guswa, A., McDonnell, J. & Villegas, J. (2012) Organization of complexity in water limited ecohydrology. Ecohydrology, 5, 184-199.
22. King, R., Morgan, B.J.T., Gimenez, O. & Brooks, S.P. (2009) Bayesian Analysis for Population Ecology. CRC Press, Boca Raton, Florida, USA.
23. Larcher, W. (1995) Physiological Plant Ecology. Springer, Berlin.
24. Law, R., Illian, J.B., Burslem, D.F.R.P., Gratzer, G., Gunatilleke, C.V.S. & Gunatilleke, I.A.U.N. (2009) Ecological information from spatial patterns of plants: insights from point process theory. Journal of Ecology, 97, 616-628.
25. Lin, Y., Chang, L., Yang, K., Wang, H. & Sun, I. (2011) Point patterns of tree distribution determined by habitat heterogeneity and dispersal limitation. Oecologia, 165, 175-184.
26. Lindgren, F., Rue, H. & Lindström, J. (2011) An explicit link between Gaussian fields and Gaussian Markov random fields: the SPDE approach. Journal of the Royal Statistical Society, Series B, 73, 423-498.
27. Martínez, I., Wiegand, T., González-Taboada, F. & Obeso, J.R. (2010) Spatial associations among tree species in a temperate forest community in north-western Spain. Forest Ecology and Management, 260, 456-465.
28. Møller, J., Syversveen, A.R. & Waagepetersen, R.P. (1998) Log Gaussian Cox processes. Scandinavian Journal of Statistics, 25, 451-482.
29. Møller, J. & Waagepetersen, R.P. (2004) Statistical Inference and Simulation for Spatial Point Processes. Chapman & Hall/CRC, Boca Raton, Florida, USA.
30. Møller, J. & Waagepetersen, R.P. (2007) Modern statistics for spatial point processes (with discussion). Scandinavian Journal of Statistics, 34, 643-711.
31. Muñoz Vallés, S., Gallego-Fernández, J. & Dellafiore, C. (2009) Estudio florístico de la flecha litoral de el rompido (lepe, huelva) análisis y catálogo de la flora vascular de los sistemas de duna y marisma. Lagascalia, 29, 43-88.
32. Muñoz Vallés, S., Gallego-Fernández, J., Dellafiore, C. & Cambrollé, J. (2011) Effects on soil, microclimate and vegetation of the native-invasive Retama monosperma (L.) in coastal dunes. Plant Ecology, 212, 169-179.
33. Myllymäki, M. & Penttinen, A. (2009) Conditionally heteroscedastic intensity-dependent marking of log Gaussian Cox processes. Statistica Neerlandica, 63, 450-473.
34. Neeff, T., Biging, G.S., Dutra, L.V., Freitas, C.C. & dos Santos, J.R. (2005) Markov point processes for modeling of spatial forest patterns in Amazonia derived from interferometric height. Remote Sensing of Environment, 97, 484-494.
35. Parra, R., Valdés, B., Ocaña, M.E. & Díaz Lifante, M.J. (2000) Thymus carnosus Boiss. Libro Rojo de la Flora Silvestre Amenazada de Andalucía, Tomo II, 11, 355-357.
36. Perry, G.L.W., Enright, N.J., Miller, B.P. & Lamont, B.B. (2008) Spatial patterns in species-rich sclerophyll shrublands of southwestern Australia. Journal of Vegetation Science, 19, 705-716.
37. Reynolds, T.J., King, R., Harwood, J., Frederikesen, M., Harris, M.P. & Wanless, S. (2009) Integrated data analyses in the presence of emigration and tag-loss. Journal of Agricultural, Biological, and Environmental Statistics, 14, 411-431.
38. Rodriguez-Iturbe, I., Porporato, A., Laio, F. & Ridolfi, L. (2001) Intensive or extensive use of soil moisture: plant strategies to cope with stochastic water availability. Geophysical Research Letters, 28, 4495-4497.
39. Rue, H. & Held, L. (2005) Gaussian Markov Random Fields. Chapman & Hall/CRC, Boca Raton, Florida, USA.
40. Rue, H., Martino, S. & Chopin, N. (2009) Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations (with discussion). Journal of the Royal Statistical Society B, 71, 319-392.
41. Schiffers, K., Schurr, F.M., Tielbörger, K., Urbach, C., Moloney, K. & Jeltsch, F. (2008) Dealing with virtual aggregations - a new index for analysing heterogeneous point patterns. Ecography, 31, 545-555.
42. Simpson, D., Illian, J., Lindgren, F., Sørbye, S.H. & Rue, H. (2011) Going off grid: computationally efficient inference for log-Gaussian Cox processes. Technical Report, Trondheim University.
43. Spiegelhalter, D.J., Best, N.G., Carlin, B.P. & van der Linde, A. (2002) Bayesian measures of model complexity and fit (with discussion). Journal of the Royal Statistical Society, Series B, 64, 583-616.
44. Viola, F., Daly, E., Vico, G., Cannarozzo, M. & Porporato, A. (2008) Transient soil-moisture dynamics and climate change in mediterranean ecosystems. Water Resources Research, 44, W11412.
45. Wang, X., Wiegand, T., Hao, Z., Li, B., Ye, J. & Lin, F. (2010) Species associations in an old-growth temperate forest in north-eastern China. Journal of Ecology, 98, 674-686.
46. Wiegand, T. & Moloney, K. (2004) Rings, circles, and null-models for point pattern analysis in ecology. Oikos, 104, 209-229.
47. Wiegand, T., Gunatilleke, S., Gunatilleke, N. & Okuda, T. (2007) Analysing the spatial structure of a Sri Lankan tree species with multiple scales of clustering. Ecology, 88, 3088-3012.
48. Zhang, J., Song, B., Li, B.-H., Ye, J., Wang, X.-G. & Hao, Z.-Q. (2010) Spatial patterns and associations of six congeneric species in an old-growth temperate forest. Acta Oecologica, 36, 29-38.
49. Zunzunegui, M., Caldeira-Díaz-Barradas, M.C. & Novo, F.G. (2000) Different phenotypic response of Halimium halimifolium in relation to groundwater availability. Plant Ecology, 148, 165-174.
50. Zunzunegui, M., Esquivias, M.P., Oppo, F. & Gallego-Fernández, J.B. (2012) Interspecific competition and livestock disturbance control the spatial pattern of two coastal dune shrubs. Plant and Soil, 354, 299-309.