phyloendemism: Phylogenetic Endemism of ecological samples

In davidnipperess/PDcalc: An implementation of the Phylogenetic Diversity (PD) calculus in R

Description

Calculates phylogenetic endemism (sum of 'unique' branch lengths) of multiple ecological samples.

Usage

phyloendemism(x, phy, weighted = TRUE)

Arguments

x	is the community data given as a data.frame or matrix with species/OTUs as columns and samples/sites as rows (like in the vegan package). Columns are labelled with the names of the species/OTUs. Rows are labelled with the names of the samples/sites. Data can be either abundance or incidence (0/1). Column labels must match tip labels in the phylogenetic tree exactly!
phy	is a rooted phylogenetic tree with branch lengths stored as a phylo object (as in the ape package) with terminal nodes labelled with names matching those of the community data table. Note that the function trims away any terminal taxa not present in the community data table, so it is not necessary to do this beforehand.
weighted	is a logical indicating whether weighted endemism (default) or strict endemism should be calculated.

Details

Takes a community data table and a rooted phylogenetic tree (with branch lengths) and calculates either strict or weighted endemism in Phylogenetic Diversity (PD). Strict endemism equates to the total amount of branch length found only in the sample/site and is described by Faith et al. (2004) as PD-endemism. Weighted endemism calculates the "spatial uniqueness" of each branch in the tree by taking the reciprocal of its range, multiplying by branch length and summing for all branch lengths present at a sample/site. Range is calculated simply as the total number of samples/sites at which the branch is present. This latter approach is described by Rosauer et al. (2009) as Phylogenetic endemism.

Value

A vector object giving the phylogenetic endemism of all sample/sites in x.

References

• Faith, Reid & Hunter. 2004. Integrating phylogenetic diversity, complementarity, and endemism for conservation assessment. Conservation Biology 18(1): 255-261.

• Rosauer, Laffan, Crisp, Donnellan & Cook. 2009. Phylogenetic endemism: a new approach for identifying geographical concentrations of evolutionary history. Molecular Ecology 18(19): 4061-4072.

davidnipperess/PDcalc documentation built on July 7, 2021, 1:07 p.m.