sim6: Sim6 Co-occurrence Randomization Algorithm

In EcoSimR: Null Model Analysis for Ecological Data

Description

Randomizes a binary matrix speciesData by reshuffling all elements. Rows are equiprobable, and columns are proportional to column sums. Makes a call to the vector_sample function.

Usage

sim6(speciesData)

Arguments

speciesData

binary presence-absence matrix (rows = species, columns = sites).

Details

This algorithm assumes that species are equiprobable, but that differences in suitability among sites are proportional to observed species richness (=colsums).

Value

Returns a binary presence-absence matrix with the same dimensions and fill as the input matrix.

Note

This algorithm assumes that species are equiprobable, and that differences among sites are proportional to observed species richness (=colsums). sim6 has a high frequency of Type I errors with random matrices, so it is not recommended for co-occurrence analysis.

References

Gotelli, N.J. 2000. Null model analysis of species co-occurrence patterns. Ecology 81: 2606-2621.

Examples

randomMatrix <- sim6(speciesData = matrix(rbinom(40,1,0.5),nrow=8))

EcoSimR documentation built on May 2, 2019, 7:26 a.m.