randomizing a community phylogenetics matrix: '3x' of Hardy (2008)

Description

resamp.3x is used for resampling data within a community dataset

Usage

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resamp.3x(obj, level=0.1)

Arguments

obj

a community dataset in spacodiR format (see as.spacodi)

level

a proportion specifying the extent of data shuffling

Details

A resampling procedure for a species-by-plots matrix, based on Gotelli swapping. Shuffles abundances within species and for a pair of plots. The level defines the degree of sampling, with larger values dictating a higher level of reshuffling. For instance, if level = 0.1 and the dataset involves 20 species and 20 plots, a total of 40 (0.1x20x20) Gotelli-like swaps are performed. The number of swaps is always rounded up such that at least one swap is performed (i.e., when level=0).

Value

A shuffled dataset

Author(s)

Jonathan Eastman

References

HARDY OJ. 2008. Testing the spatial phylogenetic structure of local communities: statistical performances of different null models and test statistics on a locally neutral community. Journal of Ecology 96:914-926.

GOTELLI NJ. 2000. Null model analysis of species co-occurrence patterns. Ecology 81:2606-2621.

See Also

spacodi.by.nodes for permutation tests of community diversity and additional randomization methods; see spacodi.calc for the main underlying function; randomizeMatrix

Examples

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data(sp.example)
attach(sp.example)
spl

# shuffle dataset
resamp.3x(obj=spl, level=0.2) 

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