metricTester (version 1.3.6)

pscCorr: Calculate corrected PSC

Description

Given a phylo object and a picante-style community data matrix (sites are rows, species are columns), calculated corrected phylogenetic species clustering

Usage

pscCorr(samp, tree)

Arguments

samp

A picante-style community data matrix with sites as rows, and species as columns

tree

Phylo object

Value

A data frame of correctly calculated PSC values, with associated species richness and name of all communities in input cdm

Details

Returns the inverse of psc as defined in picante

References

Helmus, M.R., T.J. Bland, C.K. Williams, & A.R. Ives. 2007. Phylogenetic measures of biodiversity. The American Naturalist. 169:E69-E83.

Examples

# NOT RUN {
#simulate tree with birth-death process
tree <- geiger::sim.bdtree(b=0.1, d=0, stop="taxa", n=50)

sim.abundances <- round(rlnorm(5000, meanlog=2, sdlog=1)) + 1

cdm <- simulateComm(tree, richness.vector=10:25, abundances=sim.abundances)

results <- pscCorr(samp=cdm, tree=tree)
# }