di2multi.simmap: Collapse or resolve polytomies in a tree with a character painted on the edges

Description

Collapses or resolves polytomies in special types of phylogenetic trees. (See di2multi and multi2di.)

Usage

# S3 method for simmap
di2multi(phy, ...)
# S3 method for simmap
multi2di(phy, ...)
# S3 method for multiSimmap
di2multi(phy, ...)
# S3 method for multiSimmap
multi2di(phy, ...)
# S3 method for contMap
di2multi(phy, ...)
# S3 method for contMap
multi2di(phy, ...)
# S3 method for densityMap
di2multi(phy, ...)
# S3 method for densityMap
multi2di(phy, ...)

Value

An object of class "simmap", "multiSimmap", "contMap", or "densityMap", depending on the class of phy.

Arguments

phy: object of class "simmap", "multiSimmap", "contMap", or "densityMap" containing a character mapped onto the edges of a tree or set of trees.
...: optional arguments: tol, length below which edges should be treated as having zero length; and random, specifying whether to resolve polytomies randomly (if TRUE) or in the order in which they are encountered.

Author

Liam Revell liam.revell@umb.edu

Details

The method di2multi collapses branches of zero length (or, more specifically, branches with length shorter than tol) to create a polytomy in a tree or set of trees.

The method multi2di resolves polytomies by adding branches of zero length (while preserving the mappings) in a tree or set of trees.

This methods should theoretically behave similarly to di2multi and multi2di from the ape package.

References

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