Hierarchical Bayesian models in ecology: Reconstructing species interaction networks from non-homogeneous species abundance data

Ecological Informatics

Volumn 11, Issue , 2012, Pages 55-64

  Aderhold, Andrej ^a   Husmeier, Dirk ^b,e   Lennon, Jack J ^c   Beale, Colin M ^d   Smith, V Anne ^a  

^a UNIVERSITY OF ST ANDREWS   (United Kingdom)

^b UNIVERSITY OF GLASGOW   (United Kingdom)

^c SCOTTISH CROP RESEARCH INSTITUTE   (United Kingdom)

^d UNIVERSITY OF YORK   (United Kingdom)

^e BIOMATHEMATICS AND STATISTICS SCOTLAND   (United Kingdom)

Author keywords

Bayesian hierarchical model; Multiple changepoint process; Niche model; Plant ground coverage data; Reversible jump Markov chain Monte Carlo; Species interactions

Indexed keywords

ABUNDANCE; AUTOCORRELATION; BAYESIAN ANALYSIS; CLIMATE EFFECT; COMPETITION (ECOLOGY); ECOLOGICAL MODELING; FACILITATION; HIERARCHICAL SYSTEM; INTERSPECIFIC INTERACTION; MARKOV CHAIN; MODEL TEST; MONTE CARLO ANALYSIS; MUTUALISM; NICHE; PERFORMANCE ASSESSMENT; PLANT COMMUNITY; PREDATION; RECONSTRUCTION; REGRESSION ANALYSIS; SPECIES DIVERSITY; TROPHIC INTERACTION; VEGETATION COVER;

SCOTLAND; UNITED KINGDOM; WESTERN ISLES;

EID: 84865187909     PISSN: 15749541     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ecoinf.2012.05.002     Document Type: Article

References (47)

1. Amstrup S., Marcot B., Douglas D. A Bayesian network modeling approach to forecasting the 21st century worldwide status of polar bears. Arctic sea ice decline: observations, projections, mechanisms, and implications. Geophysics Monograph Series 2008, 180:213-268.
2. Andrieu C., Doucet A. Joint Bayesian model selection and estimation of noisy sinusoids via reversible jump MCMC. IEEE Transactions on Signal Processing 1999, 47(10):2667-2676.
3. Beisner B.E., Haydon D.T., Cuddington K. Alternative stable states in ecology. Frontiers in Ecology and the Environment 2003, 1(7):376-382.
4. Bruno J.F., Stachowicz J.J., Bertness M.D. Inclusion of facilitation into ecological theory. Evolution 2003, 18(3):119-125.
5. Callaway R., Walker L. Competition and facilitation: a synthetic approach to interactions in plant communities. Ecology 1997, 78(7):1958-1965.
6. Cheney K., CÔté I. Mutualism or parasitism? The variable outcome of cleaning symbioses. Biology Letters 2005, 1(2):162-165.
7. Choler P., Michalet R., Callaway R. Facilitation and competition on gradients in alpine plant communities. Ecology 2001, 82(12):3295-3308.
8. Dahlgren J.P. Alternative regression methods are not considered in Murtaugh (2009) or by ecologists in general. Ecology Letters 2010, 13(5):E7-E9. (May).
9. Dale M.R.T., Fortin M.J. Spatial autocorrelation and statistical tests in ecology. Ecoscience 2002, 9(2):162-167.
10. Davis J., Goadrich M. The relationship between precision-recall and ROC curves. Proc. of Int. Conf. on Machine Learning 2006, 233-240. ACM.
11. Dunne J.A., Williams R.J., Martinez N.D. Network structure and biodiversity loss in food webs: robustness increases with connectance. Ecology Letters 2002, 5:558-567.
12. Faisal A., Dondelinger F., Husmeier D., Beale C. Inferring species interaction networks from species abundance data: a comparative evaluation of various statistical and machine learning methods. Ecological Informatics 2010, 5(6):451-464.
13. Foley J.A., DeFries R., Asner G.P., Barford C., Bonan G., Carpenter S.R., Chapin F.S., Coe M.T., Daily G.C., Gibbs H.K., Helkowski J.H., Holloway T., Howard E.A., Kucharik C.J., Monfreda C., Patz J.A., Prentice I.C. Global consequences of land use. Science 2005, 309:570-574.
14. Friedman N., Linial M., Nachman I., Pe'er D. Using Bayesian networks to analyze expression data. Journal of Comparative Biology 2000, 7:601-620.
15. Grandvalet Y. Least absolute shrinkage is equivalent to quadratic penalization. Perspectives in Neural Computing 1998, Vol. 1:201-206. Springer. L. Niklasson, M. Bodén, T. Ziemske (Eds.).
16. Green P. Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika 1995, 82:711-732.
17. Grzegorczyk M., Husmeier D. Non-homogeneous dynamic Bayesian networks for continuous data. Machine Learning 2011, 83(3):355-419.
18. Grzegorczyk M., Husmeier D. Bayesian regularization of non-homogeneous dynamic Bayesian networks by coupling interaction parameters. Fifth Int. Conf. on Artificial Intelligence and Statistics 2012, to appear.
19. Hagemeijer W.J.M., Blair M.J. The EBCC Atlas of European Breeding Birds: Their Distribution and Abundance 1997, Poyser, London.
20. Hartemink, A.J., 2001. Principled computational methods for the validation and discovery of genetic regulatory networks. Ph.D. thesis, MIT.
21. Hastie T., Tibshirani R., Friedman J. The Elements of Statistical Learning 2001, Springer-Verlag.
22. Henneman M.L., Memmott J. Infiltration of a Hawaiian community by introduced biological control agents. Science 2001, 293(5533):1314-1316.
23. Lande R., Engen S., Saether B.E. Stoch. Pop. Dyn. in Ecol. and Cons. 2003, Oxford University Press.
24. Lèbre S., Becq J., Devaux F., Stumpf M.P.H., Lelandais G. Statistical inference of the time-varying structure of gene-regulation networks. BMC Systems Biology 2010, 4:130.
25. Lennon J.J. Red-shifts and red herrings in geographical ecology. Ecography 2000, 23:101-113.
26. Lennon J., Beale C., Reid C., Kent M., Pakeman R. Are richness patterns of common and rare species equally well explained by environmental variables. Ecography 2011, 34:529-539.
27. Maestre F., Valladares F., Reynolds J. Is the change of plant-plant interactions with abiotic stress predictable? A meta-analysis of field results in arid environments. Journal of Ecology 2005, 93(4):748-757.
28. Maestre F., Callaway R., Valladares F., Lortie C. Refining the stress-gradient hypothesis for competition and facilitation in plant communities. Journal of Ecology 2009, 97(2):199-205.
29. Memmott J., Fowler S., Paynter Q., Sheppard A., Syrett P. The invertebrate fauna on broom, Cytisus scoparius, in two native and two exotic habitats. Acta Oecologica 2000, 21(3):213-222.
30. Milns I., Beale C.M., Smith V.A. Revealing ecological networks using Bayesian network inference algorithms. Ecology 2010, 91:1892-1899.
31. O'Gorman E.J., Emmerson M.C. Perturbations to trophic interactions and the stability of complex food webs. Proceedings of the National Academy of Sciences of the United States of America 2009, 106(32):13393-13398. (Aug.).
32. Prill R.J., Marbach D., Saez-Rodriguez J., Sorger P.K., Alexopoulos L.G., Xue X., Clarke N.D., Altan-Bonnet G., Stolovitzky G. Towards a rigorous assessment of systems biology models: the DREAM3 challenges. PloS One 2010, 5(2):e9202. (02).
33. Punskaya E., Andrieu C., Doucet A., Fitzgerald W. Bayesian curve fitting using MCMC with applications to signal segmentation. IEEE Transactions on Signal Processing 2002, 50(3):747-758.
34. Roy D.M., Teh Y.W. The Mondrian process. Proc. of Advances in Neural Information Processing Systems (NIPS) 2008, vol. 21.
35. Schmitz O.J., Krivan V., Ovadia O. Trophic cascades: the primacy of trait-mediated indirect interactions. Ecology Letters 2004, 7(2):153-163.
36. Smith V., Yu J., Smulders T., Hartemink A., Jarvis E. Computational inference of neural information flow networks. PLoS Computational Biology 2006, 2(11):1436-1449.
37. Sudderth E., Jordan M. Shared segmentation of natural scenes using dependent Pitman-Yor processes. Advances in Neural Information Processing Systems 2009, 21:1585-1592.
38. Tibshirani R. Regression shrinkage and selection via the LASSO. Journal of the Royal Statistical Society, Series B 1996, 58(1):267-288.
39. Tibshirani R. Regression shrinkage and selection via the LASSO: a retrospective (with comments). Journal of the Royal Statistical Society, Series B 2011, 73(3):273-282.
40. Tibshirani R., Walther G., Hastie T. Estimating the number of clusters in a data set via the gap statistic. Journal of the Royal Statistical Society: Series B (Statistical Methodology) 2001, 63(2):411-423.
41. Valiente-Banuet A., Verdú M. Temporal shifts from facilitation to competition occur between closely related taxa. Journal of Ecology 2008, 96(3):489-494.
42. van Oijen M., Cameron D., Reinds G., Thomson A. Bayesian methods for spatial upscaling of process-based forest ecosystem models. AGU Fall Meeting Abstracts 2010, Vol. 1:04.
43. van Someren E.P., et al. Least absolute regression network analysis of the murine osteoblast differentiation network. Bioinformatics 2006, 22(4):477-484.
44. van Veen F.J., Brandon C.E., Godfray H.C. A positive trait-mediated indirect effect involving the natural enemies of competing herbivores. Oecologia 2009, 160(1):195-205.
45. Werner E.E., Peacor S.D. A review of trait-mediated indirect interactions in ecological communities. Ecology 2003, 84(5):1083-1100.
46. Williams R.J., Martinez N.D. Simple rules yield complex food webs. Nature 2000, 404(6774):180-183.
47. Yu J., Smith V., Wang P., Hartemink A., Jarvis E. Advances to Bayesian network inference for generating causal networks from observational biological data. Bioinformatics 2004, 20(18):3594-3603. Dec.