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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.

See also

Author

Klaus Schliep klaus.schliep@gmail.com

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)