adephylo (version 1.1-16)

.tipToRoot: Low-level auxiliary functions for adephylo

Description

These hidden functions are utils for adephylo, used by other functions. Regular users can use them as well, but no validity checks are performed for the arguments: speed is here favored over safety. Most of these functions handle trees inheriting phylo4 class.

Usage

.tipToRoot(x, tip, root, include.root = FALSE)

Value

.tipToRoot: a vector of named integers identifying nodes.

Arguments

x

A valid tree of class phylo4.

tip

An integer identifying a tip by its numbers.

root

An integer identifying the root of the tree by its number.

include.root

a logical stating whether the root must be included as a node of the path from tip to root (TRUE), or not (FALSE, default).

Author

Thibaut Jombart

Details

.tipToRoot finds the set of nodes between a tip and the root of a tree.

Examples

if(require(ape) & require(phylobase)){
## make a tree
x <- as(rtree(20),"phylo4")
plot(x,show.node=TRUE)

## .tipToRoot
root <- rootNode(x)
.tipToRoot(x, 1, root)
lapply(1:nTips(x), function(i) .tipToRoot(x, i, root))
}