phyloTop (version 2.1.2)

pitchforks: Number of pitchforks

Description

Finds the number of pitchforks in a tree. A pitchfork is considered to be a clade with three tips.

Usage

pitchforks(tree, normalise = FALSE)

Value

An integer representing the number of pitchforks in the tree.

Arguments

tree

a tree of class phylo or phylo4. The tree should be binary and rooted; if not it will be coerced into a binary rooted tree using multi2di, if possible.

normalise

option to normalise the result, default is FALSE.

Author

Michelle Kendall

See Also

configShow

Examples

## Find the number of pitchforks in a random tree with 20 tips:
tree <- rtree(20)
plot(tree)
pitchforks(tree)
# and the normalised pitchfork number:
pitchforks(tree, normalise=TRUE)

## Note that the function configShow can be used to highlight the pitchforks in the tree:
configShow(tree, 3, edge.width=2)