Uncovering hidden spatial structure in species communities with spatially explicit joint species distribution models

Summary Modern species distribution models account for spatial autocorrelation in order to obtain unbiased statistical inference on the effects of covariates, to improve the model's predictive ability through spatial interpolation and to gain insight in the spatial processes shaping the data. Somewhat analogously, hierarchical approaches to community‐level data have been developed to gain insights into community‐level processes and to improve species‐level inference by borrowing information from other species that are either ecologically or phylogenetically related to the focal species. We unify spatial and community‐level structures by developing spatially explicit joint species distribution models. The models utilize spatially structured latent factors to model missing covariates as well as species‐to‐species associations in a statistically and computationally effective manner. We illustrate that the inclusion of the spatial latent factors greatly increases the predictive performance of the modelling approach with a case study of 55 species of butterfly recorded on a 10 km × 10 km grid in Great Britain consisting of 2609 grid cells.