picante (version 0.7-1)

specaccum.psr: 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.

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