getRoot: Tree manipulation

Description

midpoint performs midpoint rooting of a tree. pruneTree produces a consensus tree. 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 by default assumes that node labels contain support values. This works if support values are computed from splits, but should be recomputed for clades. keep_as_tip takes a list of tips and/or node labels and returns a tree pruned to those. If node label, then it prunes all descendants of that node until that internal node becomes a tip.

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 = ">=")
keep_as_tip(tree, labels)

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.
labels: tip and node labels to keep as tip labels in the tree

Author

Klaus Schliep klaus.schliep@gmail.com

Examples

Run this code


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)