phytools (version 2.1-1)

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, ...)

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).

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.

Author

Liam Revell

Details

The function nodeHeights also gives a handy way to get the total length of the tree from the root to the highest 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, whereas nodeheight will be faster if the height of one or a small number of nodes are needed.

References

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

See Also

vcvPhylo

Examples

## load tree
data(vertebrate.tree)
## compute height of all nodes
H<-nodeHeights(vertebrate.tree)
print(H)
## compute total tree depth
max(H)