Randomize sample/community data matrices to create null distributions of given metrics
1 2 3  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")

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 
null.model 
permutation procedure used to create the null distribution, see 
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 trialswap null models, see 
alpha 
probability value to compare the observed mean/correlations to a null distribution 
fam 
as in 
The function creates null distributions for the psd
set of metrics and for the correlations of sppregs
from observed community data sets.
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 
mean.null 
mean(s) of the null distribution(s) 
quantiles.null 
quantiles of the null distribution(s) to compare to 
phylo.structure 
if 
nulls 
null values of the distribution(s) 
Matthew Helmus mrhelmus@gmail.com
Helmus M.R., Bland T.J., Williams C.K. & Ives A.R. (2007a) Phylogenetic measures of biodiversity. American Naturalist, 169, E68E83
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, 917925
Gotelli N.J. (2000) Null model analysis of species cooccurrence patterns. Ecology, 81, 26062621
psd
,sppregs
, randomizeMatrix
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