metricTester (version 1.2.2)

modifiedMPD: Calculate different versions of abundance-weighted MPD

Description

Given a picante-style community data matrix (sites are rows, species are columns), a phylogenetic distance matrix, and a desired method of abundance-weighting, will calculate MPD.

Usage

modifiedMPD(samp, dis, abundance.weighted = FALSE)

Arguments

samp

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

dis

Phylogenetic distance matrix

abundance.weighted

One of either "FALSE", "interspecific", "intraspecific", or "complete"

Value

A vector of MPD values, calculated according to the abundance-weighted method specified.

Details

See accompanying publication for details. Non-abundance-weighted and interspecific and intraspecific methods are equivalent to those previously described by Clarke & Warwick.

References

Miller, E. T., D. R. Farine, and C. H. Trisos. 2015. Phylogenetic community structure metrics and null models: a review with new methods and software. bioRxiv 025726.

Examples

#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)

dists <- ape::cophenetic.phylo(tree)

results <- modifiedMPD(cdm, dists, abundance.weighted = "interspecific")