sim1: Sim1 Co-occurrence Randomization Algorithm
In EcoSimR: Null Model Analysis for Ecological Data

Description Usage Arguments Details Value Note References Examples

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

1	sim1(speciesData)

speciesData

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

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

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

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.

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