- tre
: a character string of the phylogenetic tree in Newick format whithout branch length values

- leaves
: a vector which names corresponds to leaves and values gives the distance between leaves and nodes closest to these leaves

- nodes
: a vector which names corresponds to nodes and values gives the distance between nodes and nodes closest to these leaves

- parts
: a list which elements gives the direct descendants of each nodes

- paths
: a list which elements gives the path leading from the root to taxonomic units (leaves and nodes)

- droot
: a vector which names corresponds to taxonomic units and values gives distance between taxonomic units and the root

- call
: call

- Wmat
: a phylogenetic link matrix, generally called the covariance matrix. Matrix values \(Wmat_{ij}\) correspond to path length that lead from root to the first common ancestor of the two leaves i and j

- Wdist
: a phylogenetic distance matrix of class `'dist'`

. Matrix values \(Wdist_{ij}\) correspond to \(\sqrt{d_{ij}}\) where \(d_{ij}\) is the classical distance between two leaves i and j

- Wvalues
: a vector with the eigen values of Wmat

- Wscores
: a data frame with eigen vectors of Wmat. This data frame defines an orthobasis that could be used to calculate the orthonormal decomposition of a biological trait on a tree.

- Amat
: a phylogenetic link matrix stemed from Abouheif's test and defined in Ollier et al. (submited)

- Avalues
: a vector with the eigen values of Amat

- Adim
: number of positive eigen values

- Ascores
: a data frame with eigen vectors of Amat. This data frame defines an orthobasis that could be used to calculate the orthonormal decomposition of a biological trait on a tree.

- Aparam
: a data frame with attributes associated to nodes.

- Bindica
: a data frame giving for some taxonomic units the partition of leaves that is associated to its

- Bscores
: a data frame giving an orthobasis defined by Ollier et al. (submited) that could be used to calculate the orthonormal decomposition of a biological trait on a tree.

- Bvalues
: a vector giving the degree of phylogenetic autocorrelation for each vectors of Bscores (Moran's form calculated with the matrix Wmat)

- Blabels
: a vector giving for each nodes the name of the vector of Bscores that is associated to its