randomizeSample function

Null models for community data matrix randomization

Various null models for randomizing community data matrices

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

Returns

Randomized community data matrix

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

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.

Author(s)

Steven Kembel steve.kembel@gmail.com

Examples

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