Randomize sample/community data matrices to create null distributions of given metrics
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")community data matrix, species as columns, communities as rows
phylo tree object or a phylogenetic covariance matrix
environmental data matrix
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
permutation procedure used to create the null distribution, see randomizeMatrix
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
probability value to compare the observed mean/correlations to a null distribution
as in sppregs
metric used
permutation used
number of permutations
number of swaps if applicable
observed mean value of a particular metric or the three observed correlations from sppregs
mean(s) of the null distribution(s)
quantiles of the null distribution(s) to compare to obs; determined by alpha
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"
null values of the distribution(s)
The function creates null distributions for the psd set of metrics and for the correlations of sppregs from observed community data sets.
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