ec_cooc_count_pair: Co-occurrence network

In KevCaz/ecoocc: Occurrence, co-occurrence and more

Co-occurrence network

Description

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

Usage

ec_cooc_count_pair(x)

ec_cooc_count_triplet(x)

ec_checkerboard(x)

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

• ec_cooc_count_pair(): A matrix with all pairs of species and the corresponding co-occurrence counts.

• ec_cooc_count_triplet(): A matrix with all triplets of species and the corresponding co-occurrence counts.

• ec_checkerboard(): Compute the checkerboard score and return a list of three elements:

  • units which incudes checkerboard units and t

  • c_score checkerboard scores.

  • c_score_s2 the S2 statistics in Roberts & Stone (1990).

References

• Veech, J. A. (2013). A probabilistic model for analysing species co-occurrence: Probabilistic model. Global Ecology and Biogeography, 22(2), 252–260.

• Arita, H. T. (2016). Species co-occurrence analysis: Pairwise versus matrix-level approaches: Correspondence. Global Ecology and Biogeography, 25(11), 1397–1400.

• Stone, L., & Roberts, A. (1990). The checkerboard score and species distributions. Oecologia, 85(1), 74–79. https://doi.org/10.1007/BF00317345

• Roberts, A., & Stone, L. (1990). Island-sharing by archipelago species. Oecologia, 83(4), 560–567. https://doi.org/10.1007/BF00317210

Examples

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 May 24, 2023, 1:43 p.m.