phylog {ade4} | R Documentation

## Phylogeny

### Description

Create and use objects of class `phylog`.
`phylog.extract` returns objects of class `phylog`. It extracts sub-trees from a tree.
`phylog.permut` returns objects of class `phylog`. It creates the different representations compatible with tree topology.

### Usage

    print.phylog(x, ...)
    phylog.extract(phylog, node, distance = TRUE)
    phylog.permut(phylog, list.nodes = NULL, distance = TRUE))

### Arguments

`x, phylog` | : an object of class `phylog`
`...` | : further arguments passed to or from other methods
`node` | : a string of characters giving a node name. The functions extracts the tree rooted at this node.
`distance` | : if TRUE, both functions retain branch lengths. If FALSE, they returns tree with arbitrary branch lengths (each branch length equals one)
`list.nodes` | : a list which elements are vectors of string of character corresponding to direct descendants of nodes. This list defines one representation compatible with tree topology among the set of possibilities.

### Value

Returns a list of class `phylog` :

`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

### Author(s)

Daniel Chessel chessel@biomserv.univ-lyon1.fr
Sébastien Ollier ollier@biomserv.univ-lyon1.fr

### References

Ollier, S., Pontier, D. and Chessel, D. (submitted) Comments on Abouheif's test. Evolutionary Ecology Research.

Ollier, S., Couteron, P. and Chessel, D. (submitted) Orthonormal transforms to detect and describe phylogenetic autocorrelation. Biometrics.

### See Also

`newick2phylog`, `plot.phylog`

### Examples

    marthans.tre <- NULL
    marthans.tre[1] <-"((((1:4,2:4)a:5,(3:7,4:7)b:2)c:2,5:11)d:2,"
    marthans.tre[2] <- "((6:5,7:5)e:4,(8:4,9:4)f:5)g:4);"
    marthans.phylog <- newick2phylog(marthans.tre)
    marthans.phylog

    if (require(ape, quietly=TRUE)) {
    marthans.phylo <- read.tree(text = marthans.tre)
    marthans.phylo

    par(mfrow =c (1,2))
    plot.phylog(marthans.phylog, cnode = 3, f = 0.8, cle = 3)
    plot.phylo(marthans.phylo)
    par(mfrow = c(1,1))
    }

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