We have developed a general class of joint species distribution modes, called “Hierarchical Modelling of Species Communities” (HMSC), that make it possible to integrate data on species occurrence, environmental covariates, species traits, and phylogenetic relationships in a statistically efficient and ecologically informed way. The framework applies to many kinds of data, including hierarchical, spatially explicit, and temporally explicit study designs, and e.g. presence-absence data or abundance data. As special cases, HMSC includes single species distribution models and model-based ordinations.
Warton, D., Blanchet, G., O’Hara, R., Ovaskainen, O., Taskinen, S., Walker, S. and Hui, F. K. C. 2015. So many variables: joint modelling in community ecology. Trends in Ecology and Evolution 30, 766-779
Ovaskainen, O., Roy, D., Fox, R. and Anderson, B. 2016. Uncovering hidden spatial structure in species communities with spatially explicit joint species distribution models. Methods in Ecology and Evolution 7, 428-436.
Ovaskainen, O., Abrego, N., Halme, P. and Dunson, D. 2016. Using latent variable models to identify large networks of species-to-species associations at different spatial scales. Methods in Ecology and Evolution 7, 549-555.