specaccum.psr: Phylogenetic Species Richness Sample-Based Rarefaction Curve

In picante: R tools for integrating phylogenies and ecology

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 [e-mail] 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

Examples

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"))

Example output

Loading required package: ape
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-3
Loading required package: nlme
Set of permutations < 'minperm'. Generating entire set.

picante documentation built on May 2, 2019, 6:30 p.m.