Description Usage Arguments Details Value Author(s) References See Also Examples
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).
1 |
x |
a tree of class |
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 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
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 |
Loading required package: ade4
Loading required package: ape
Loading required package: phylobase
Attaching package: 'phylobase'
The following object is masked from 'package:ape':
edges
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.