Sim3 Co-occurrence Randomization Algorithm
Randomizes a binary matrix speciesData by reshuffling elements within each column equiprobably.
binary presence-absence matrix (rows = species, columns = sites).
This algorithm assumes species are equiprobable, but preserves differences among sites (= column sums).
Returns a binary presence-absence matrix with the same dimensions and colsums as the input matrix.
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.
Gotelli, N.J. 2000. Null model analysis of species co-occurrence patterns. Ecology 81: 2606-2621.
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