Teasing apart the effects of environmental variations and biotic interactions on species distributions
ELGRIN jointly models the presence and absence of all species in a given area in function of environmental covariates and the topological structure of the known metaweb
elgrin(presence, metaweb, environmentvar, ncores=1)
presence: A matrix with presence/absence of species (rows) at different locations (columns), coded in 0/1 format (1 for presence).metaweb: A matrix or a igraph object. This represents the metaweb/metawnetwork of interactions as an adjacency matrix or as a graph respectively.environmentvar: A matrix with environmental variables (columns) at different locations (rows).ncores: The number of cores to use, i.e. at most how many threads will run simultaneously. Default is 1 (no parallelization).ELGRIN (in reference to Charles Elton and Joseph Grinnell) can handle the effects of both environmental factors and known ecological interactions (aka a metanetwork) on species distributions. We rely on Markov random fields, a family of flexible models that can handle dependencies between variables using a graph.
elgrin returns an object of class list with the following components: - a: A vector of species intercepts.
al: A vector of location intercepts.
b: A matrix of linear environmental parameters.
c: A matrix of quadratic environmental parameters.
betaPres: A vector of co-presence strength (or avoidance when <0) at each location.
betaAbs: A vector of co-absence strength (or avoidance when <0) at each location.
compat: A matrix with niche compatibility of species (rows) at different locations (columns), coded in 0/1 format (1 for compatibility)..
Vincent Miele, Catherine Matias, Marc Ohlmann, Giovanni Poggiato, St ephane Dray and Wilfried Thuiller, Quantifying the overall effect of biotic1interactions on species communities along2environmental gradients, arXiv doi:10.48550/arXiv.2103.10433
Authors: Vincent Miele Maintainer: Vincent Miele vincent.miele@univ-lyon1.fr
data(virtualComCompetition) vcom <- virtualComCompetition result <- elgrin(vcom$presence, vcom$metaweb, vcom$environmentvar) str(result) plot(result$betaPres, result$betaAbs, xlab="Co-presence", ylab="Co-absence") abline(h=0, col=2) abline(v=0, col=2)