sim4: Sim4 Co-occurrence Randomization Algorithm

In EcoSimR: Null Model Analysis for Ecological Data

Description

Randomizes a binary matrix speciesData by reshuffling elements within each row. Sampling weights for each column are proportional to column sums. Makes a call to the vector_sample function.

Usage

sim4(speciesData)

Arguments

speciesData

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

Details

This algorithm preserves differences among species in occurrence frequencies, but assumes differences among sites in suitability are proportional to observed species richness (= column sums).

Value

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

Note

This algorithm preserves differences in the commonness and rarity of species (= rowsums), but assumes differences among sites in suitability are proportional to observed species richness (= column sums). sim4 has a somewhat 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 <- sim4(speciesData = matrix(rbinom(40,1,0.5),nrow=8))

EcoSimR documentation built on May 2, 2019, 7:26 a.m.