di2multi.simmap {phytools} | R Documentation |
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 class 'simmap'
di2multi(phy, ...)
## S3 method for class 'simmap'
multi2di(phy, ...)
## S3 method for class 'multiSimmap'
di2multi(phy, ...)
## S3 method for class 'multiSimmap'
multi2di(phy, ...)
## S3 method for class 'contMap'
di2multi(phy, ...)
## S3 method for class 'contMap'
multi2di(phy, ...)
## S3 method for class 'densityMap'
di2multi(phy, ...)
## S3 method for class 'densityMap'
multi2di(phy, ...)
Arguments
phy |
object of class |
... |
optional arguments: |
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.
Value
An object of class "simmap"
, "multiSimmap"
, "contMap"
, or "densityMap"
, depending on the class of phy
.
Author(s)
Liam Revell liam.revell@umb.edu
References
Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.
See Also
contMap
, densityMap
, di2multi
, make.simmap
, multi2di
, read.simmap