Explicit Interaction Community Models

Model fitting and species biotic interaction network topology selection for explicit interaction community models. Explicit interaction community models are an extension of binomial linear models for joint modelling of species communities, that incorporate both the effects of species biotic interactions and the effects of missing covariates. Species interactions are modelled as direct effects of each species on each of the others, and are estimated alongside the effects of missing covariates, modelled as latent factors. The package includes a penalized maximum likelihood fitting function, and a genetic algorithm for selecting the most parsimonious species interaction network topology.

eicm (R package)

Explicit Interaction Community Models

Available on CRAN, can be directly installed from within R.

Model fitting and species biotic interaction network topology selection for EICMs. EICMs are an extension of binomial GLMs for joint modelling of species communities, that incorporate both the effects of species biotic interactions and the effects of missing covariates. Species interactions are modelled as direct effects of each species on each of the others, and are estimated alongside the effects of missing covariates, modelled as latent factors. The package includes a Penalized Maximum Likelihood fitting function, and a Genetic Algorithm for selecting the most parsimonious species interaction network topology.