randomizeSample: Null models for community data matrix randomization

In picante: R tools for integrating phylogenies and ecology

Description

Various null models for randomizing community data matrices

Usage

randomizeMatrix(samp, null.model = c("frequency", "richness",
    "independentswap", "trialswap"), iterations = 1000)    

Arguments

samp	Community data matrix
null.model	Null model to use (see Details section for description)
iterations	Number of independent or trial-swaps to perform

Details

Currently implemented null models (arguments to null.model):

frequency

Randomize community data matrix abundances within species (maintains species occurence frequency)

richness

Randomize community data matrix abundances within samples (maintains sample species richness)

independentswap

Randomize community data matrix with the independent swap algorithm (Gotelli 2000) maintaining species occurrence frequency and sample species richness

trialswap

Randomize community data matrix with the trial-swap algorithm (Miklos & Podani 2004) maintaining species occurrence frequency and sample species richness

Value

Randomized community data matrix

Author(s)

Steven Kembel <[e-mail]>

References

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

Miklos I. & Podani J. 2004. Randomization of presence-absence matrices: Comments and new algorithms. Ecology 85: 86-92.

Examples

data(phylocom)
randomizeMatrix(phylocom$sample, null.model="richness")

picante documentation built on May 2, 2019, 6:30 p.m.