# phylog

From ade4 v1.3-3
by Jean Thioulouse

##### Phylogeny

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.

- Keywords
- manip

##### 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 $d_{ij} $ where $d_{ij}$ is the classical distance between two leaves i and jWvalues : 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

##### 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

##### 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))
}
```

*Documentation reproduced from package ade4, version 1.3-3, License: GPL version 2 or newer*

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