miscUtils: Low-level auxiliary functions for adephylo

In adephylo: Exploratory Analyses for the Phylogenetic Comparative Method

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)

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).

Details

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

Value

.tipToRoot: a vector of named integers identifying nodes.

Author(s)

Thibaut Jombart [e-mail]

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))
}

adephylo documentation built on Oct. 6, 2023, 5:07 p.m.