bind.tree: Binds Trees

In ape: Analyses of Phylogenetics and Evolution

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

x	an object of class "phylo".
y	an object of class "phylo".
where	an integer giving the number of the node or tip of the tree x where the tree y is binded ("root" is a short-cut for the root).
position	a numeric value giving the position from the tip or node given by node where the tree y is binded; negative values are ignored.
interactive	if TRUE the user is asked to choose the tip or node of x by clicking on the tree which must be plotted.

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.

Value

an object of class "phylo".

Author(s)

Emmanuel Paradis

See Also

drop.tip, root

Examples

### binds the two clades of bird orders
treefile1 <- tempfile("tree", fileext = ".tre")
treefile2 <- tempfile("tree", fileext = ".tre")
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 = treefile1, 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 = treefile2, sep = "\n")
tree.bird1 <- read.tree(treefile1)
tree.bird2 <- read.tree(treefile2)
unlink(c(treefile1, treefile2)) # 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)")

## make sure the terminal branch length is long enough:
x$edge.length[x$edge[, 2] == 2] <- 0.2

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)

ape documentation built on May 29, 2024, 10:50 a.m.