Characterising uncertainty in generalised dissimilarity models

Methods in Ecology and Evolution

Volumn 8, Issue 8, 2017, Pages 985-995

  Woolley, Skipton N C ^a,b   Foster, Scott D ^c   O'Hara, Timothy D ^a   Wintle, Brendan A ^b   Dunstan, Piers K ^c  

^a MUSEUMS VICTORIA   (Australia)

^b UNIVERSITY OF MELBOURNE   (Australia)

^c CSIRO   (Australia)

Author keywords

Bayesian bootstrap; beta diversity; community ecology; generalised additive models; generalised linear models

Indexed keywords

EID: 85013018496     PISSN: None     EISSN: 2041210X     Source Type: Journal    
DOI: 10.1111/2041-210X.12710     Document Type: Article

References (44)

1. Akaike, H. (1974) A new look at the statistical model identification. IEEE Transactions on Automatic Control, 19, 716–723.
2. Anderson, M.J. (2004) DISTLM v.5: a FORTRAN computer program to calculate a distance-based multivariate analysis for a linear model. Department of Statistics, University of Auckland, New Zealand, 10, 2016.
3. Davison, A.C. (1997) Bootstrap methods and their application. Technometrics, 42, 582.
4. Diego, S., Barbara, S., Regan, H.M., Ben-Haim, Y., Langford, B., Wilson, W.G., Lundberg, P., Andelman, S.J. & Burgman, M.A. (2005) Robust decision-making under severe uncertainty for conservation management. Ecological Applications, 15, 1471–1477.
5. Dunlop, M., Hilbert, D., Ferrier, S. & House, A. (2012) The Implications of Climate Change for Biodiversity Conservation and the National Reserve System: Final Synthesis. CSIRO, Canberra, Australia.
6. Dunn, P.K. & Smyth, G.K. (1996) Randomized quantile residuals. Journal of Computational and Graphical Statistics, 5, 236–244.
7. Dunstan, P.K. & Foster, S.D. (2011) RAD biodiversity: prediction of rank abundance distributions from deep water benthic assemblages. Ecography, 34, 798–806.
8. Dunstan, P.K., Foster, S.D. & Darnell, R. (2011) Model based grouping of species across environmental gradients. Ecological Modelling, 222, 955–963.
9. Dunstan, P.K., Althaus, F., Williams, A. & Bax, N.J.(2012a) Characterising and predicting benthic biodiversity for conservation planning in deepwater environments. PLoS ONE, 7, e36558.
10. Dunstan, P.K., Bax, N.J., Foster, S.D., Williams, A. & Althaus, F. (2012b) Identifying hotspots for biodiversity management using rank abundance distributions. Diversity and Distributions, 18, 22–32.
11. Ferrari, S.L.P. & Cribari-Neto, F. (2004) Beta regression for modelling rates and proportions. Journal of Applied Statistics, 31, 799–815.
12. Ferrier, S., Drielsma, M., Manion, G. & Watson, G. (2002) Extended statistical approaches to modelling spatial pattern in biodiversity in northeast New South Wales. II. Community-level modelling. Biodiversity and Conservation, 11, 2309–2338.
13. Ferrier, S., Manion, G., Elith, J. & Richardson, K. (2007) Using generalized dissimilarity modelling to analyse and predict patterns of beta diversity in regional biodiversity assessment. Diversity and Distributions, 13, 252–264.
14. Fitzpatrick, M.C., Sanders, N.J., Normand, S., Svenning, J.C., Ferrier, S., Gove, A.D. & Dunn, R.R. (2013) Environmental and historical imprints on beta diversity: insights from variation in rates of species turnover along gradients. Proceedings Biological Sciences/The Royal Society, 280, 20131201.
15. Foster, S.D. & Dunstan, P.K. (2010) The analysis of biodiversity using rank abundance distributions. Biometrics, 66, 186–195.
16. Foster, S.D., Shimadzu, H. & Darnell, R. (2012) Uncertainty in spatially predicted covariates: is it ignorable? Journal of the Royal Statistical Society Series C: Applied Statistics, 61, 637–652.
17. Foster, S.D., Givens, G.H., Dornan, G.J., Dunstan, P.K. & Darnell, R. (2013) Modelling biological regions from multi-species and environmental data. Environmetrics, 24, 489–499.
18. GA (2009) Australian Bathymetry and Topography Grid. Geoscience Australia, Canberra, Australia.
19. Gelman, A., Carlin. J., Stern, H., Dunson, D., Ventari, A. & Rubin, D. (2013) Bayesian Data Analysis, volume 2. Chapman & Hall/CRC, Boca Raton, FL, USA.
20. Guisan, A. & Zimmermann, N.E. (2000) Predictive habitat distribution models in ecology. Ecological Modelling, 135, 147–186.
21. Jaccard, P. (1912) The distribution of the flora in the alpine zone.1. New Phytologist, 11, 37–50.
22. Jones, M.M., Gibson, N., Yates, C., Ferrier, S., Mokany, K., Williams, K.J., Manion, G. & Svenning, J.C. (2015) Underestimated effects of climate on plant species turnover in the Southwest Australian Floristic Region. Journal of Biogeography, 43, 289–300.
23. Kodde, D.A. & Palm, F.C. (1986) Wald criteria for jointly testing equality and inequality restrictions. Econometrica, 54, 1243–1248.
24. Koslow, J.A., Gowlett-Holmes, K., Lowry, J.K., O'Hara, T., Poore, G.C.B. & Williams, A. (2001) Seamount benthic macrofauna off southern Tasmania: community structure and impacts of trawling. Marine Ecology Progress Series, 213, 111–125.
25. Leathwick, J.R. & Elith, J. (2009) Species distribution models: ecological explanation and prediction across space and time. Annual Review of Ecology and Systematics, 40, 415–436.
26. Leathwick, J.R., Snelder, T., Chadderton, W.L., Elith, J., Julian, K. & Ferrier, S. (2011) Use of generalised dissimilarity modelling to improve the biological discrimination of river and stream classifications. Freshwater Biology, 56, 21–38.
27. Lewis, M. (1999) CSIRO-SEBS (Seamount, Epibenthic Sampler), a new epibenthic sled for sampling seamounts and other rough terrain. Deep-Sea Research Part I: Oceanographic Research Papers, 46, 1101–1107.
28. McCullagh, P. & Nelder, J. (1989) Generalized Linear Models, 2nd edn. Chapman & Hall, London, UK.
29. Ovaskainen, O., Hottola, J. & Shtonen, J. (2010) Modeling species co-occurrence by multivariate logistic regression generates new hypotheses on fungal interactions. Ecology, 91, 2514–2521.
30. Polasky, S., Carpenter, S.R., Folke, C. & Keeler, B. (2011) Decision-making under great uncertainty: Environmental management in an era of global change. Trends in Ecology and Evolution, 26, 398–404.
31. Pya, N. & Wood, S.N. (2014) Shape constrained additive models. Statistics and Computing, 25, 1–17.
32. Ramsay, J.O. (1988) Monotone regression splines in action. Statistical Science, 3, 425–441.
33. Ridgway, K.R., Dunn, J.R. & Wilkin, J.L. (2002) Ocean interpolation by four-dimensional weighted least squares – application to the waters around Australasia. Journal of Atmospheric and Oceanic Technology, 19, 1357–1375.
34. Rubin, D.B. (1981) The bayesian bootstrap. The Annals of Statistics, 9, 130–134.
35. Schwarz, G. (1978) Estimating the dimension of a model. The Annals of Statistics, 6, 461–464.
36. Smouse, P.E., Long, J.C. & Sokal, R.R. (1986) Multiple regression and correlation extensions of the mantel test of matrix correspondence. Systematic Zoology, 35, 627.
37. Stoklosa, J., Daly, C., Foster, S.D., Ashcroft, M.B. & Warton, D.I. (2015) A climate of uncertainty: Accounting for error in climate variables for species distribution models. Methods in Ecology and Evolution, 6, 412–423.
38. Warton, D.I., Wright, S.T. & Wang, Y. (2012) Distance-based multivariate analyses confound location and dispersion effects. Methods in Ecology and Evolution, 3, 89–101.
39. Warton, D.I., Foster, S.D., De'ath, G., Stoklosa, J. & Dunstan, P.K. (2015) Model-based thinking for community ecology. Plant Ecology, 216, 669–682.
40. Williams, A., Koslow, J.A. & Last, P.R. (2001) Diversity, density and community structure of the demersal fish fauna of the continental slope off Western Australia (20 to 35S). Marine Ecology Progress Series, 212, 247–263.
41. Williams, A., Althaus, F., Dunstan, P.K., Poore, G.C.B., Bax, N.J., Kloser, R.J. & McEnnulty, F.R. (2010a) Scales of habitat heterogeneity and megabenthos biodiversity on an extensive Australian continental margin (100–1100-m depths). Marine Ecology, 31, 222–236.
42. Williams, A., Schlacher, T.A., Rowden, A.A. et al. (2010b) Seamount megabenthic assemblages fail to recover from trawling impacts. Marine Ecology, 31, 183–199.
43. Wintle, B.A., McCarthy, M.A., Volinsky, C.T. & Kavanagh, R.P. (2003) The use of bayesian model averaging to better represent uncertainty in ecological models. Conservation Biology, 17, 1579–1590.
44. Wintle, B.A., Bekessy, S.A., Keith, D.A. et al. (2011) Ecological economic optimization of biodiversity conservation under climate change. Nature Climate Change, 1, 355–359.