elgrin {econetwork} | R Documentation |
Teasing apart the effects of environmental variations and biotic interactions on species distributions
Description
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
Usage
elgrin(presence, metaweb, environmentvar, ncores=1)
Arguments
presence |
A |
metaweb |
A |
environmentvar |
A |
ncores |
The number of cores to use, i.e. at most how many threads will run simultaneously. Default is 1 (no parallelization). |
Details
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.
Value
elgrin
returns an object of class list
with the following components:
a |
A |
al |
A |
b |
A |
c |
A |
betaPres |
A |
betaAbs |
A |
compat |
A |
Author(s)
Authors: Vincent Miele Maintainer: Vincent Miele <vincent.miele@univ-lyon1.fr>
References
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>
Examples
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)