Anna Eklöf, Si Tang and Stefano Allesina
This repository includes the code for analyzing secondary extinctions in food webs using Bayesian networks. Code written by Anna Eklöf, Si Tang and Stefano Allesina.
REFERENCE: Eklöf, Anna, Si Tang, and Stefano Allesina. "Secondary extinctions in food webs: a Bayesian network approach." Methods in Ecology and Evolution 4.8 (2013): 760-770.
Please cite and acknowledge properly!
Contact: anna.eklof@liu.se
BN-Wrapper.R is where the start function is located. Function to initialize analyse is TestCode
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## INPUT
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# Adjacency: square, binary matrix
# Adjacency[i,j] = 1 means that j consumes i
# Extant: observed presence of the species
# binary, Reps x S matrix, where
# Reps is the number of observations
# and each row is a different replicate
# marking whether the species was present (1) or absent (0)
# ProbExtinction: vector of length S, measuring
# the probability that each species goes extinct due
# to external causes
# Functional: functional form, as in the paper.
# Options are "topo", "linear", and "nonlinear"
# Alpha, Beta: parameters for nonlinear functional response
# Label: label for the system
#
# Results returned as "results.Rdata" stored in "FW"
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