Biodiversity mapping functions for R (3): Phylogenetic Endemism (raw)

Phylogenetic Endemism

I am sequentially posting some self-contained functions for mapping biodiversity metrics in R, this one is:

phylogenetic.endemism.R [full code at https://raw.githubusercontent.com/GregGuerin/biomap/master/phylogenetic.endemism.R]

Description --
Calculates phylogenetic endemism (phylogenetic diversity inversely weighted by the spatial range of particular branch lengths) or alternatively (unweighted) phylogenetic diversity across gridded maps using individual or site-based point records.

Details --
This implementation of phylogenetic endemism allows alternative calculation of weights for branch length ranges. Weights can be calculated based on the frequency of occurrence in grid cells, or alternatively by the georeferenced span of the range. Unweighted phylogenetic diversity can also be selected.

Usage --
An example:

require(vegan)
data(mite)
data(mite.xy)
require(ape)
mite.tree <- rtree(n=ncol(mite), tip.label=colnames(mite)) #for this example, generate a phylogenetic tree of the species in the mite dataset with random relationships and branch lengths
####Usage of the function:
mite.PE <- phylogenetic.endemism(mite, records="site", site.coords=mite.xy, sep.comm.spp="none", phylo.tree=mite.tree, sep.phylo.spp="none", weight.type="geo")