A phylo tree object or a phylogenetic covariance matrix
permutations
Number of permutations with method method= "random"
method
Species accumulation method, currently only "random" is supported which adds samples in random order.
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Other parameters to functions
Value
The function returns an object of class "specaccum" with items:
call
Function call.
method
Accumulator method.
sites
Number of sites/samples.
richness
The mean phylogenetic species richness corresponding to number of sites/samples.
sd
The standard deviation of phylogenetic apecies accumulation curve (or its standard error) estimated from permutations in method = "random".
perm
Permutation results with method = "random" and NULL in other cases. Each column in perm holds one permutation.
Author(s)
Matthew Helmus mrhelmus@gmail.com based on the vegan package specaccum function by Roeland Kindt and Jari Oksanen.
References
Gotelli N.J. & Colwell R.K. (2001) Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness. Ecology Letters, 4, 379-391
Helmus M.R., Bland T.J., Williams C.K. & Ives A.R. (2007) Phylogenetic measures of biodiversity. American Naturalist, 169, E68-E83