bind.tree: Binds Trees

Description

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

Usage

bind.tree(x, y, node = -1, branch = NULL, position = NULL)

Arguments

an object of class "phylo".

node

a negative integer giving the node number of the tree x where the tree y is binded (by default -1, i.e. the root).

branch

an integer; if specified this gives the number of a tip or of a label of the tree x below which the tree y is binded.

position

a numeric value giving the position from the tip or node given by branch where the tree y is binded.

Value

an object of class "phylo".

Details

The argument node is ignored if branch is given. The argument x can be seen as the receptor tree, whereas y is the donor tree. The root of y is then sticked on a location of x specified by either the argument node, or the arguments branch and position. If y has a root edge, this is added as in internal branch in the resulting tree.

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 <- 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)