phylostruct: 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 produ

null.model

permutation procedure used to create the null distribution, see randomizeMatrix

runs

the number of permutations to create the distribution, a rule of thumb is (number of communities)/alpha

the number of swaps for the independent and trial-swap null models, see randomizeMatrix

alpha

probability value to compare the observed mean/correlations to a null distribution

fam

as in sppregs

Value

metricmetric used
null.modelpermutation used
runsnumber of permutations
itnumber of swaps if applicable
obsobserved mean value of a particular metric or the three observed correlations from sppregs
mean.nullmean(s) of the null distribution(s)
quantiles.nullquantiles of the null distribution(s) to compare to obs; determined by alpha
phylo.structureif 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"
nullsnull values of the distribution(s)

Details

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

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

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