ec_cooc_count_pair: Co-occurrence network

Description Usage Arguments Details Functions References Examples

View source: R/ec_cooccurrence.R

Description

Compute the co-occurrence between all pairs of species and descriptive metrics of the co-occurrence network.

Usage

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Arguments

x

a pa object or an R object to a coerced to one (see ec_as_pa()).

Details

Currently bi tests the presence of a significant value of occurrence assuming species occurrence are independent 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 both species relatively low, then bi and hy give very similar results.

Functions

References

Examples

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mat <- ec_generate_pa(1000, 6, .2)
out <- ec_cooc_count_pair(mat)
#plot(out$zs_bi*sqrt(1/0.2), out$zs_hy)
#abline(0,1)

# Classical example, in Stone & Roberts 1990
mat0 <- matrix(0, 10, 10)
mat1 <- matrix(1, 10, 10)
matU <- rbind(cbind(mat1, mat0), cbind(mat0, mat1))
ec_checkerboard(matU)

KevCaz/ecoocc documentation built on Aug. 7, 2021, 8:22 p.m.