Explicit Interaction Community Models
Define a parameterized EICM model
Extract EICM model coefficients
Diagnostic monitor plots for EICM
Confidence intervals for EICM parameters
eicm: Explicit Interaction Community Models
Define a data object for a EICM model
Estimate a EICM model
Define a model object for a EICM model
Set EICM fitting options
Fit and select an Explicit Interaction Community Model (EICM)
Generate EICM model following a Beta frequency distribution
Compare two interaction matrices
Is the adjacency matrix a cyclic graph?
EICM (penalized) log-likelihood
Plot EICM estimates and confidence intervals
Quick plot EICM results
Quick plot EICM results
Plot EICM likelihood profile
Plot graphs from adjacency matrices
Predict method for EICM fits
Print EICM model matrix
Likelihood profiles for EICMs
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.