phylog | R Documentation |

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.

## S3 method for class 'phylog' print(x, ...) phylog.extract(phylog, node, distance = TRUE) phylog.permut(phylog, list.nodes = NULL, distance = TRUE)

`x, phylog` |
: an object of class |

`...` |
: 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. |

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 |

`Wdist` |
: a phylogenetic distance matrix of class |

`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 |

Daniel Chessel

Sébastien Ollier sebastien.ollier@u-psud.fr

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.

`newick2phylog`

, `plot.phylog`

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)) }

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