phylodiv: Phylogenetic Diversity of ecological samples

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

Description

Calculates the Phylogenetic Diversity (PD) of multiple samples simultaneously. Note that this function uses that version of PD that always includes the path to the root of the tree.

Usage

phylodiv(x, phy)

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.

Details

phylodiv takes community data and a phylogenetic tree (rooted and with branch lengths) and calculates the Phylogenetic Diversity (PD) of all samples/sites. PD is defined as the total length of all branches spanning a set of terminal taxa representing an ecological sample (Faith, 1992). Please note that, if the common ancestor (node) of the set of taxa of a sample is not the root of the tree, then the set of branches connecting this node to the root are also included in the calculation. Calculations are achieved using the efficient matrix algebra solution of Rodrigues & Gaston (2002).

Value

A vector of Phylogenetic Diversity (PD) values for each sample/site in x.

References

• Faith DP. 1992. Conservation evaluation and phylogenetic diversity. Biological Conservation 61: 1-10.

• Rodrigues A & Gaston KJ. 2002. Maximising phylogenetic diversity in the selection of networks of conservation areas. Biological Conservation 105: 103-111.

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