midpoint: Tree manipulation

In phangorn: Phylogenetic Reconstruction and Analysis

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 class 'phylo'
midpoint(tree, node.labels = "support", ...)

## S3 method for class 'multiPhylo'
midpoint(tree, node.labels = "support", ...)

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

keep_as_tip(tree, labels)

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

Value

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

Author(s)

Klaus Schliep [e-mail]

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)

phangorn documentation built on Sept. 17, 2024, 5:08 p.m.