R: Calculate different versions of abundance-weighted MPD
modifiedMPD
R Documentation
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.
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"
Details
See accompanying publication for details. Non-abundance-weighted and
interspecific and intraspecific methods are equivalent to those previously described by
Clarke & Warwick.
Value
A vector of MPD values, calculated according to the abundance-weighted method
specified.
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")