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.

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

Examples

Run this code

# NOT RUN {
data(phylocom)
accum.sr<-specaccum(phylocom$sample, permutations = 100, method = "random")
plot(accum.sr, col="blue")
points(accum.sr$sites, accum.sr$richness, pch=19, col="blue")

accum.psr<-specaccum.psr(phylocom$sample, phylocom$phylo, permutations = 100, method = "random")
plot(accum.psr, add=TRUE, col = "red")
points(accum.psr$sites, accum.psr$richness, pch=19, col="red")

legend(5,5,legend=c("SR","PSR"),pch=c(19,19),col=c("blue","red"))
# }