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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.

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Install

install.packages('eicm')

Monthly Downloads

219

Version

1.0.3

License

GPL (>= 2)

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Repository

https://github.com/miguel-porto/eicm

Maintainer

Miguel Porto

Last Published

May 5th, 2023

Functions in eicm (1.0.3)

A parameterized EICM model for simulation

Predict method for EICM fits

print.eicm.matrix

Print EICM model matrix

Likelihood profiles for EICMs

Define a data object for a EICM model

coefficientComparisonPlot

Diagnostic monitor plots for EICM

Define a model object for a EICM model

Set EICM fitting options

eicm: Explicit Interaction Community Models

Define a parameterized EICM model

Fit and select an Explicit Interaction Community Model (EICM)

Estimate a EICM model

Confidence intervals for EICM parameters

plotNetworkFromMatrix

Plot graphs from adjacency matrices

Generate EICM model following a Beta frequency distribution

plot.confint.eicm

Plot EICM estimates and confidence intervals

Quick plot EICM results

Quick plot EICM results

plot.profile.eicm

Plot EICM likelihood profile

Is the adjacency matrix a cyclic graph?

EICM (penalized) log-likelihood

Extract EICM model coefficients

interactionPlot

Compare two interaction matrices