Phylogenetic Species Richness Sample-Based Rarefaction Curve
Finds a sample-based rarefaction curve for phylogentic species richness for a set of samples.
specaccum.psr(samp, tree, permutations = 100, method = "random", ...)
samp |
Community data matrix |
tree |
A phylo tree object or a phylogenetic covariance matrix |
permutations |
Number of permutations with method |
method |
Species accumulation method, currently only |
... |
Other parameters to functions |
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 |
perm |
Permutation results with |
Matthew Helmus mrhelmus@gmail.com based on the vegan package specaccum function by Roeland Kindt and Jari Oksanen.
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
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"))Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.