treePart {adephylo} | R Documentation |
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).
treePart(x, result=c("dummy", "orthobasis"))
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 ). |
Orthobasis produced by this function are identical to those stored in the $Bscores component of deprecated phylog objects, from the ade4 package.
A matrix of numeric vectors (in columns) having one value for each tip (rows).
Thibaut Jombart tjombart@imperial.ac.uk
Ollier, S., Chessel, D. and Couteron, P. (2005) Orthonormal Transform to Decompose the Variance of a Life-History Trait across a Phylogenetic Tree. Biometrics, 62, 471–477.
- listDD
which is called by treePart
.
- orthogram
, which uses by default the orthobasis
produced by treePart
.
if(require(ape) & require(phylobase)){ ## make a tree x <- as(rtree(10),"phylo4") partition <- treePart(x) partition ## plot the dummy vectors with the tree temp <- phylo4d(x, partition) table.phylo4d(temp, cent=FALSE, scale=FALSE) } if(require(ade4)){ ## former orthobasis in ade4 data(ungulates) ung.Bscores <- newick2phylog(ungulates$tre)$Bscores ## version using treePart ung <- read.tree(text=ungulates$tre) ung.orthobas <- treePart(ung, res="orthobasis") ## comparison of the first 3 vectors cbind(ung.Bscores[,1], ung.orthobas[,1],ung.Bscores[,2], ung.orthobas[,2], ung.Bscores[,3], ung.orthobas[,3]) }