specaccum.psr {picante}R Documentation

Phylogenetic Species Richness Sample-Based Rarefaction Curve

Description

Finds a sample-based rarefaction curve for phylogentic species richness for a set of samples.

Usage

specaccum.psr(samp, tree, permutations = 100, method = "random", ...)

Arguments

samp Community data matrix
tree 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.
... 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

See Also

psr, specaccum


[Package picante version 0.6-1 Index]