Sim3 Co-occurrence Randomization Algorithm

Usage

sim3(speciesData)

Arguments

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

Value

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

Description

Randomizes a binary matrix speciesData by reshuffling elements within each column equiprobably.

Details

This algorithm assumes species are equiprobable, but preserves differences among sites (= column sums).

Note

This algorithm preserves differences in species richness among sites (= colsums), but assumes that all species are equiprobable. This assumption is usually unrealistic, and sim3 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 <- sim3(speciesData=matrix(rbinom(40,1,0.5),nrow=8))