Joint Species Distribution Modelling (JSDM) is becoming an increasingly popular statistical method for analyzing data in community ecology.
JSDM allow the integration of community ecology data with data on environmental covariates, species traits, phylogenetic relationships, and the spatio-temporal context of the study, providing predictive insights into community assembly processes from non-manipulative observational data of species communities. Hierarchical Modelling of Species Communities (HMSC) is a general and flexible framework for fitting JSDMs, yet its full range of functionality has remained restricted to Matlab users only.
The package, along with the extended vignettes, makes JSDM fitting and post-processing easily accessible to ecologists familiar with R. We illustrate the use of the package by providing a series of five vignettes that apply HMSC-R 3.0 to simulated and real data.
https://www.helsinki.fi/en/researchgroups/statistical-ecology/hmsc