phytools: nodeHeights – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

nodeHeights

Compute the heights above the root of each node

Description

nodeHeights computes the height above the root for all nodes in the tree. nodeheight computes the height above the root for a single node.

Usage

nodeHeights(tree, ...)
nodeheight(tree, node, ...)

Arguments

`tree`	a phylogeny as an object of class `"phylo"`.
`node`	for `nodeheight`, the node for which we want to compute a height above the root (or including the root edge, for `root.edge=TRUE`).
`...`	optional arguments - presently only `root.edge`, a logical value indicating whether or not to include the root edge length in the calculation of node heights.

Details

The function nodeHeights also gives a handy way to get the total length of the tree from the root to the heighest tip which will be given by max(nodeHeights(tree)). Generally speaking, nodeHeights will be faster if the heights of all or a large proportion of nodes is needed, wherease nodeheight will be faster if the height of one or a small number of nodes are needed.

Value

Either a matrix of the same dimensions as tree$edge containing the height above the root of each node in edge (for nodeHeights); or a single positive number (for nodeheight).

Author(s)

Liam Revell liam.revell@umb.edu

References

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.

Examples

tree<-rtree(10)
X<-nodeHeights(tree)

phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

v0.7-70

GPL (>= 2)

Authors

Liam J. Revell

Initial release

2020-9-19