1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
|
\name{untangle}
\alias{untangle}
\title{Attempts to untangle crossing branches for plotting}
\usage{
untangle(tree, method=c("reorder","read.tree"))
}
\arguments{
\item{tree}{tree as an object of class \code{"phylo"} or \code{"simmap"}.}
\item{method}{method to use to attempt to untangle branches. \code{method="reorder"} uses two calls of \code{\link[ape]{reorder.phylo}} or \code{\link{reorderSimmap}}; \code{method="read.tree"} writes the tree to a text string and then reads it back into memory using \code{\link[ape]{read.tree}}.}
}
\description{
Attempts to "untangle" the branches of a tree that are tangled when plotting with \code{\link[ape]{plot.phylo}}, \code{\link{plotTree}}, or \code{\link{plotSimmap}}.
}
\details{
Generally speaking, this function is wraps several different internal functions that might be use to fix a badly conformed \code{"phylo"} or \code{"simmap"} object.
}
\value{
An object of class \code{"phylo"} or \code{"simmap"}, depending on the class of \code{tree}.
}
\references{
Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). \emph{PeerJ}, \bold{12}, e16505.
}
\author{Liam Revell \email{liam.revell@umb.edu}}
\keyword{phylogenetics}
\keyword{utilities}
|
