R: Phylogeny

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

    ## S3 method for class 'phylog'
    print(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 √{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
Sébastien Ollier sebastien.ollier@u-psud.fr

### References

Ollier, S., Couteron, P. and Chessel, D. (2006) Orthonormal transform to decompose the variance of a life-history trait across a phylogenetic tree. Biometrics Biometrics, 62, 2, 471–477.

### 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(requireNamespace("ape", quietly = TRUE)) {
      marthans.phylo <- ape::read.tree(text = marthans.tre)
      marthans.phylo

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

[Package ade4 version 1.7-16 Index]