https://github.com/cran/ape
Tip revision: 856dc17b51b415ee05514d54fb4ee6b7af8822ae authored by Emmanuel Paradis on 20 December 2004, 00:00:00 UTC
version 1.4
version 1.4
Tip revision: 856dc17
bind.tree.Rd
\name{bind.tree}
\alias{bind.tree}
\title{Binds Trees}
\usage{
bind.tree(x, y, node = -1, branch = NULL, position = NULL)
}
\arguments{
\item{x}{an object of class \code{"phylo"}.}
\item{y}{an object of class \code{"phylo"}.}
\item{node}{a negative integer giving the node number of the tree
\code{x} where the tree \code{y} is binded (by default -1, i.e. the
root).}
\item{branch}{an integer; if specified this gives the number of a tip
or of a label of the tree \code{x} below which the tree \code{y} is
binded.}
\item{position}{a numeric value giving the position from the tip or
node given by \code{branch} where the tree \code{y} is binded.}
}
\description{
This function binds together two phylogenetic trees to result in a
single object of class \code{"phylo"}.
}
\details{
The argument \code{node} is ignored if \code{branch} is given. The
argument \code{x} can be seen as the receptor tree, whereas \code{y}
is the donor tree. The root of \code{y} is then sticked on a location
of \code{x} specified by either the argument \code{node}, or the
arguments \code{branch} and \code{position}. If \code{y} has a root
edge, this is added as in internal branch in the resulting tree.
}
\value{
an object of class \code{"phylo"}.
}
\author{Emmanuel Paradis \email{paradis@isem.univ-montp2.fr}}
\seealso{
\code{\link{drop.tip}}, \code{\link{root}}, \code{\link{rotate}}
}
\examples{
### binds the two clades of bird orders
cat("((Struthioniformes:21.8,Tinamiformes:21.8):4.1,",
"((Craciformes:21.6,Galliformes:21.6):1.3,Anseriformes:22.9):3.0):2.1;",
file = "ex1.tre", sep = "\n")
cat("(Turniciformes:27.0,(Piciformes:26.3,((Galbuliformes:24.4,",
"((Bucerotiformes:20.8,Upupiformes:20.8):2.6,",
"(Trogoniformes:22.1,Coraciiformes:22.1):1.3):1.0):0.6,",
"(Coliiformes:24.5,(Cuculiformes:23.7,(Psittaciformes:23.1,",
"(((Apodiformes:21.3,Trochiliformes:21.3):0.6,",
"(Musophagiformes:20.4,Strigiformes:20.4):1.5):0.6,",
"((Columbiformes:20.8,(Gruiformes:20.1,Ciconiiformes:20.1):0.7):0.8,",
"Passeriformes:21.6):0.9):0.6):0.6):0.8):0.5):1.3):0.7):1.0;",
file = "ex2.tre", sep = "\n")
tree.bird1 <- read.tree("ex1.tre")
tree.bird2 <- read.tree("ex2.tre")
unlink(c("ex1.tre", "ex2.tre")) # clean-up
birds <- bind.tree(tree.bird1, tree.bird2, branch = -1,
position = tree.bird1$root.edge)
birds
layout(matrix(c(1, 2, 3, 3), 2, 2))
plot(tree.bird1)
plot(tree.bird2)
plot(birds)
layout(matrix(1))
}
\keyword{manip}