Sim7 Co-occurrence Randomization Algorithm

Usage

sim7(speciesData)

Arguments

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

Value

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

Description

Randomizes a binary matrix speciesData by reshuffling all elements. Columns are equiprobable, and rows are proportional to row sums. Makes a call to the vector_sample function.

Details

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

Note

This algorithm assumes that species are equiprobable, and that differences among sites are proportional to observed species richness (=colsums). sim7 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 <- sim7(speciesData = matrix(rbinom(40,1,0.5),nrow=8))