sim1: Sim1 Co-occurrence Randomization Algorithm

Description Usage Arguments Details Value Note References Examples

View source: R/algorithms.R

Description

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

Usage

1
sim1(speciesData)

Arguments

speciesData

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

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.

Value

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

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

1
randomMatrix <- sim1(speciesData=matrix(rbinom(40,1,0.5),nrow=8))

EcoSimR documentation built on May 29, 2017, 9:11 p.m.