phangorn (version 2.1.1)

midpoint: Tree manipulation

Description

midpoint performs midpoint rooting of a tree. pruneTree produces a consensus tree.

Usage

midpoint(tree, node.labels = "support")
pruneTree(tree, ..., FUN = ">=")
getRoot(tree)

Arguments

tree

an object of class phylo

FUN

a function evaluated on the nodelabels, result must be logical.

node.labels

are nodel labels 'support' values, 'label' or should be 'deleted'

...

further arguments, passed to other methods.

Value

pruneTree and midpoint a tree. getRoot returns the root node.

Details

pruneTree prunes back a tree and produces a consensus tree, for trees already containing nodelabels. It assumes that nodelabels are numerical or character that allows conversion to numerical, it uses as.numeric(as.character(tree$node.labels)) to convert them. midpoint so far does not transform node.labels properly.

See Also

consensus, root, di2multi

Examples

tree = unroot(rtree(10))
tree$node.label = c("", round(runif(tree$Nnode-1), 3))

tree2 = midpoint(tree)
tree3 = pruneTree(tree, .5)

par(mfrow = c(3,1))
plot(tree, show.node.label=TRUE)
plot(tree2, show.node.label=TRUE)
plot(tree3, show.node.label=TRUE)