phylostruct {picante}R Documentation

Permutations to Test for Phylogenetic Signal in Community Composition

Description

Randomize sample/community data matrices to create null distributions of given metrics

Usage

phylostruct(samp, tree, env=NULL, metric=c("psv","psr","pse","psc","sppregs"), null.model=c("frequency",
            "richness","independentswap","trialswap"), runs=100, it=1000, alpha=0.05, fam="binomial")

Arguments

samp community data matrix, species as columns, communities as rows
tree phylo tree object or a phylogenetic covariance matrix
env environmental data matrix
metric if metric="psv", "psr", "pse", or "psc" compares the observed mean of the respective metric to a null distribution at a given alpha; if metric="sppregs" compares the three correlations produced by sppregs to null distributions
null.model permutation procedure used to create the null distribution, see randomizeSample
runs the number of permutations to create the distribution, a rule of thumb is (number of communities)/alpha
it the number of swaps for the independent and trial-swap null models, see randomizeSample
alpha probability value to compare the observed mean/correlations to a null distribution
fam as in sppregs

Details

The function creates null distributions for the psd set of metrics and for the correlations of sppregs from observed community data sets.

Value

metric metric used
null.model permutation used
runs number of permutations
it number of swaps if applicable
obs observed mean value of a particular metric or the three observed correlations from sppregs
mean.null mean(s) of the null distribution(s)
quantiles.null quantiles of the null distribution(s) to compare to obs; determined by alpha
phylo.structure if obs less than (alpha/2), phylo.structure="underdispersed"; if obs greater than (1-alpha/2), phylo.structure="overdispersed"; otherwise phylo.structure="random" and NULL if metric="sppregs"
nulls null values of the distribution(s)

Author(s)

Matthew Helmus mrhelmus@gmail.com

References

Helmus M.R., Bland T.J., Williams C.K. & Ives A.R. (2007a) Phylogenetic measures of biodiversity. American Naturalist, 169, E68-E83

Helmus M.R., Savage K., Diebel M.W., Maxted J.T. & Ives A.R. (2007b) Separating the determinants of phylogenetic community structure. Ecology Letters, 10, 917-925

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

See Also

psd ,sppregs, randomizeSample


[Package picante version 0.6-1 Index]