untangle {phytools}

Attempts to untangle crossing branches for plotting

Description

Attempts to "untangle" the branches of a tree that are tangled when plotting with plot.phylo, plotTree, or plotSimmap.

Usage

untangle(tree, method=c("reorder","read.tree"))

Arguments

tree

tree as an object of class "phylo" or "simmap".

method

method to use to attempt to untangle branches. method="reorder" uses two calls of reorder.phylo or reorderSimmap; method="read.tree" writes the tree to a text string and then reads it back into memory using read.tree.

Details

Generally speaking, this function is wraps several different internal functions that might be use to fix a badly conformed "phylo" or "simmap" object.

Value

An object of class "phylo" or "simmap", depending on the class of tree.

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.