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 

result 
a character string specifying the type of result: either a
basis of dummy vectors ( 
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 LifeHistory 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
.
## 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)