picante: phylostruct – R documentation

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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 produced by `sppregs` to null distributions
`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
`it`	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`

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