phangorn (version 2.11.1)

getRoot: Tree manipulation

Description

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

Usage

getRoot(tree)
midpoint(tree, node.labels = "support", ...)
# S3 method for phylo
midpoint(tree, node.labels = "support", ...)
# S3 method for multiPhylo
midpoint(tree, node.labels = "support", ...)
pruneTree(tree, ..., FUN = ">=")

Value

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

Arguments

tree

an object of class phylo.

node.labels

are node labels 'support' values (edges), 'label' or should labels get 'deleted'?

...

further arguments, passed to other methods.

FUN

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

Author

Klaus Schliep

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, multi2di

Examples

tree <- rtree(10, rooted = FALSE)
tree$node.label <- c("", round(runif(tree$Nnode-1), digits=3))

tree2 <- midpoint(tree)
tree3 <- pruneTree(tree, .5)

old.par <- par(no.readonly = TRUE)
par(mfrow = c(3,1))
plot(tree, show.node.label=TRUE)
plot(tree2, show.node.label=TRUE)
plot(tree3, show.node.label=TRUE)
par(old.par)