EcoSimR 0.1.0

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Sim1 Co-occurrence Randomization Algorithm

Usage

sim1(speciesData)

Arguments

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

Value

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

Description

Randomizes a binary matrix speciesData by reshuffling all of its elements equiprobably.

Details

This algorithm assumes species and sites are equiprobable. It preserves the total matrix fill, but places no other constraints on row or column totals.

Note

This is the simplest of all randomization algorithms for a presence- absence matrix. However, it assumes that both species and sites are equiprobable, and has poor Type I error frequencies when tested with purely random matrices. If the input matrix is sparse, it will often generate null matrices with empty rows or columns. 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 <- sim1(speciesData=matrix(rbinom(40,1,0.5),nrow=8))