phangorn (version 1.99-1)

midpoint: Tree manipulation

Description

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

Usage

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

Arguments

tree

an object of class phylo

FUN

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

...

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 genereated from numericals, 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)