treePart: Define partitions of tips according from a tree

In adephylo: Exploratory Analyses for the Phylogenetic Comparative Method

Define partitions of tips according from a tree

Description

The function treePart defines partitions of tips reflecting the topology of a tree. There are two possible outputs (handled by the argument result):
- basis mode: each node but the root is translated into a dummy vector having one value for each tip: this value is '1' if the tip descends from this node, and '0' otherwise.
- orthobasis: in this mode, an orthonormal basis is derived from the basis previously mentionned. This orthobasis was proposed in the orthogram (Ollier et al. 2006).

Usage

treePart(x, result = c("dummy", "orthobasis"))

Arguments

x	a tree of class phylo, phylo4 or phylo4d.
result	a character string specifying the type of result: either a basis of dummy vectors (dummy), or an orthobasis derived from these dummy vectors (orthobasis).

Details

Orthobasis produced by this function are identical to those stored in the Bscores component of deprecated phylog objects, from the ade4 package.

Value

A matrix of numeric vectors (in columns) having one value for each tip (rows).

Author(s)

Thibaut Jombart [e-mail]

References

Ollier, S., Chessel, D. and Couteron, P. (2005) Orthonormal Transform to Decompose the Variance of a Life-History Trait across a Phylogenetic Tree. Biometrics, 62, 471–477.

See Also

- listDD which is called by treePart.
- orthogram, which uses by default the orthobasis produced by treePart.

Examples

if(require(ape) & require(phylobase)){
## make a tree
x <- as(rtree(10),"phylo4")
partition <- treePart(x)
partition

## plot the dummy vectors with the tree
temp <- phylo4d(x, partition)
table.phylo4d(temp, cent=FALSE, scale=FALSE)
}

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