specaccum.psr {picante} | R Documentation |
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= "random" |
method |
Species accumulation method, currently only "random" is supported which adds samples in random order. |
... |
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 method = "random" . |
perm |
Permutation results with method = "random" and NULL in other cases. Each column in perm holds one permutation. |
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