adephylo: treePart – R documentation

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treePart

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 tjombart@imperial.ac.uk

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.

Examples

## Not run: 

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)
}

## End(Not run)

adephylo

Exploratory Analyses for the Phylogenetic Comparative Method

v1.1-11

GPL (>= 2)

Authors

Thibaut Jombart <t.jombart@imperial.ac.uk>, Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anders Ellern Bilgrau <abilgrau@math.aau.dk>

Initial release

2017-12-18