Exploratory Analyses for the Phylogenetic Comparative Method
Abouheif's test based on Moran's I
The adephylo package
Fan-like phylogeny with possible representation of traits on tips
Compute the distance of tips to the root
Compute some phylogenetic distance between tips
List direct descendants for all nodes of a tree
List tips descendings from all nodes of a tree
Low-level auxiliary functions for adephylo
Computes Moran's index for a variable
Computes Moran's eigenvectors from a tree or a phylogenetic proximity ...
Orthonormal decomposition of variance
Phylogenetic principal component analysis
Compute some phylogenetic proximities between tips
Find the shortest path between tips of a tree
Graphical display of phylogeny and traits
Define partitions of tips according from a tree
Multivariate tools to analyze comparative data, i.e. a phylogeny and some traits measured for each taxa. The package contains functions to represent comparative data, compute phylogenetic proximities, perform multivariate analysis with phylogenetic constraints and test for the presence of phylogenetic autocorrelation. The package is described in Jombart et al (2010) <doi:10.1093/bioinformatics/btq292>.