bind.tree: Binds Trees

Description

This function binds together two phylogenetic trees to give a single object of class "phylo".

Usage

bind.tree(x, y, where = "root", position = 0, interactive = FALSE)
x + y

Arguments

Value

an object of class "phylo".

Details

The argument x can be seen as the receptor tree, whereas y is the donor tree. The root of y is then grafted on a location of x specified by where and, possibly, position. If y has a root edge, this is added as in internal branch in the resulting tree.

x + y is a shortcut for:

bind.tree(x, y, position = if (is.null(x$root.edge)) 0 else x$root.edge)

If only one of the trees has no branch length, the branch lengths of the other one are ignored with a warning.

If one (or both) of the trees has no branch length, it is possible to specify a value of 'position' to graft 'y' below the node of 'x' specified by 'where'. In this case, the exact value of 'position' is not important as long as it is greater than zero. The new node will be multichotomous if 'y' has no root edge. This can be solved by giving an arbitrary root edge to 'y' beforehand (e.g., y$root.edge <- 1): it will be deleted during the binding operation.

Examples

Run this code

### 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 = "")
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 = "")
tree.bird1 <- read.tree("ex1.tre")
tree.bird2 <- read.tree("ex2.tre")
unlink(c("ex1.tre", "ex2.tre")) # clean-up
(birds <- tree.bird1 + tree.bird2)
layout(matrix(c(1, 2, 3, 3), 2, 2))
plot(tree.bird1)
plot(tree.bird2)
plot(birds)

### examples with random trees
x <- rtree(4, tip.label = LETTERS[1:4])
y <- rtree(4, tip.label = LETTERS[5:8])
x <- makeNodeLabel(x, prefix = "x_")
y <- makeNodeLabel(y, prefix = "y_")
x$root.edge <- y$root.edge <- .2

z <- bind.tree(x, y, po=.2)
plot(y, show.node.label = TRUE, font = 1, root.edge = TRUE)
title("y")
plot(x, show.node.label = TRUE, font = 1, root.edge = TRUE)
title("x")
plot(z, show.node.label = TRUE, font = 1, root.edge = TRUE)
title("z <- bind.tree(x, y, po=.2)")

z <- bind.tree(x, y, 2, .1)
plot(y, show.node.label = TRUE, font = 1, root.edge = TRUE)
title("y")
plot(x, show.node.label = TRUE, font = 1, root.edge = TRUE)
title("x")
plot(z, show.node.label = TRUE, font = 1, root.edge = TRUE)
title("z <- bind.tree(x, y, 2, .1)")

x <- rtree(50)
y <- rtree(50)
x$root.edge <- y$root.edge <- .2
z <- x + y
plot(y, show.tip.label = FALSE, root.edge = TRUE); axisPhylo()
title("y")
plot(x, show.tip.label = FALSE, root.edge = TRUE); axisPhylo()
title("x")
plot(z, show.tip.label = FALSE, root.edge = TRUE); axisPhylo()
title("z <- x + y")
layout(1)