Simulate stochastic bipartite network based on trait values of species - in R

Posted by Scott Chamberlain on Stack Overflow See other posts from Stack Overflow or by Scott Chamberlain
Published on 2012-08-27T22:46:57Z Indexed on 2012/08/28 3:38 UTC
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I would like to create bipartite networks in R. For example, if you have a data.frame of two types of species (that can only interact across species, not within species), and each species has a trait value (e.g., size of mouth in the predator allows who gets to eat which prey species), how do we simulate a network based on the traits of the species (that is, two species can only interact if their traits overlap in values for instance)?

UPDATE: Here is a minimal example of what I am trying to do. 1) create phylogenetic tree; 2) simulate traits on the phylogeny; 3) create networks based on species trait values.

# packages
install.packages(c("ape","phytools"))
library(ape); library(phytools)

# Make phylogenetic trees
tree_predator <- rcoal(10)
tree_prey <- rcoal(10)

# Simulate traits on each tree
trait_predator <- fastBM(tree_predator)
trait_prey <- fastBM(tree_prey)

# Create network of predator and prey
## This is the part I can't do yet. I want to create bipartite networks, where 
## predator and prey interact based on certain crriteria. For example, predator
## species A and prey species B only interact if their body size ratio is
## greater than X.

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