bind.tree: Binds Trees

In gjuggler/ape: Analyses of Phylogenetics and Evolution

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)
  

Value

an object of class "phylo".

Author(s)

Emmanuel Paradis

See Also

drop.tip, root

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 <- 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)

gjuggler/ape documentation built on May 17, 2019, 6:03 a.m.