ec_cooccurrence: Co-occurrence

Description Usage Arguments Details Value Author(s) References Examples

Description

Compute the co-occurrence between all pairs of species.

Usage

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ec_cooccurrence(mat_pa, test = NULL, species_names = NULL)

Arguments

mat_pa

presence absence matrix (sites as rows and species as columns).

test

test to be performed. Currenlty bi and hy are available (see details). Default is set to NULL, meaning no test is performed.

species_names

string vector giving the names of the sites. If

Details

Currently bi tests the presence of a significant value of occurrence assuming species occurrence are independant binomial distribution. by takes the limited number of sites into account by using an hypergeometric distribution (see Veech 2013). Note that if the number of sites is large and the occurrence of bith species relatively low, then bi and hy give very similar results.

Value

A matrix with species combination and co-occurrence values associated.

Author(s)

Kevin Cazelles

References

Veech, J. A.. A Probabilistic Model for Analysing Species Co-Occurrence: Probabilistic Model. Global Ecology and Biogeography (2013).

Examples

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mat <- matrix(stats::runif(60000)>.2,  ncol = 6)
out <- ec_cooccurrence(mat, test = c('bi', 'hy'))
plot(out$zs_bi*sqrt(1/0.2), out$zs_hy)
abline(0,1)

KevCaz/ecoocc documentation built on May 25, 2019, 12:22 p.m.