add.random: Add tips at random to the tree

In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

Add tips at random to the tree

Description

This function adds new tips at random to a tree with branch lengths.

Usage

add.random(tree, n=NULL, tips=NULL, edge.length=NULL, order=c("random","input"))

Arguments

tree	an object of class "phylo".
n	a number of tips to add to the tree. If NULL, will use length(tips). If tips is specified, then n is also ignored, regardless of its value.
tips	a set of tip names for the added tips. If NULL, names will be supplied
edge.length	terminal edge length for the added tips. If NULL, and is.ultrametric(tree) ==TRUE, then edge lengths will be assigned to keep the tree ultrametric. Note that if edge lengths are assigned and n>1, then the assigned terminal edge lengths are not guaranteed as subsequent random tip addition could occur along the new terminal edge.
order	addition order for the new tips.

Details

If no edge lengths are provided, and the tree is ultrametric, then edge lengths are assigned to keep the tree ultrametric.

The probability that at new tip is added along any branch is directly proportional to the length of the branch.

Note that sometimes the resultant tree plotted with plot.phylo or plotSimmap may display with branches crossing. If so, the tree can be 'untangled' using untangle.

Value

An object of class "phylo".

Author(s)

Liam Revell [e-mail]

References

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

See Also

allFurcTrees, add.everywhere

phytools documentation built on June 22, 2024, 10:39 a.m.