phylomatchr: Matches taxa in a set of sites with the tips of a...

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

Description

Matches taxa in a set of sites with the tips of a phylogenetic tree

Usage

phylomatchr(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.

Value

A list of two vectors. The first vector is the taxa found in the tree but not in the sites. The second vector is the taxa found in the sites but not in the tree.

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