treedatacheck: Checks a set of phylogenetic trees to confirm they are...

In windex: Analysing Convergent Evolution using the Wheatsheaf Index

Checks a set of phylogenetic trees to confirm they are ultrametric and binary and that tip labels match a list of names.

Description

Takes a set of phylogenetic trees as a multiPhylo object (or a single tree as a phylo object) and a vector (e.g. of species names) and reports which trees (if any) are not binary, not ultrametric, or have tip labels that don't match the vector of names.

Usage

treedatacheck(trees,species)

Arguments

trees	Set of phylogenetic trees of class 'multiPhylo' or 'phylo' containing branch lengths.
species	Vector of names to be matched against tip labels of the tree(s).

Value

Either confirms that all trees are binary, ultrametric, and have tip labels matching the list of names, or prints warnings stating which trees do not meet those criteria (with troubleshooting options for mismatches between data and single trees).

Author(s)

Kevin Arbuckle

windex documentation built on Oct. 11, 2023, 5:16 p.m.