| phylog {ade4} | 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 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. |
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 |
Daniel Chessel
Sébastien Ollier ollier@biomserv.univ-lyon1.fr
Ollier, S., Couteron, P. and Chessel, D. (2005) Orthonormal transforms to detect and describe phylogenetic autocorrelation. Biometrics (in press).
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))
}
> library(ade4)
> ### Name: phylog
> ### Title: Phylogeny
> ### Aliases: phylog print.phylog phylog.extract phylog.permut
> ### Keywords: manip
>
> ### ** 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
Phylogenetic tree with 9 leaves and 8 nodes
$class: phylog
$call: newick2phylog(x.tre = marthans.tre)
$tre: ((((X1,X2)a,(X3,X4)b)c,X5...,((X6,X7)e,(X8,X9)f)g)Root;
class length content
$leaves numeric 9 length of the first preceeding adjacent edge
$nodes numeric 8 length of the first preceeding adjacent edge
$parts list 8 subsets of descendant nodes
$paths list 17 path from root to node or leave
$droot numeric 17 distance to root
class dim content
$Wmat matrix 9-9 W matrix : root to the closest ancestor
$Wdist dist 36 Nodal distances
$Wvalues numeric 8 Eigen values of QWQ/sum(Q)
$Wscores data.frame 9-8 Eigen vectors of QWQ '1/n' normed
$Amat matrix 9-9 Topological proximity matrix A
$Avalues numeric 8 Eigen values of QAQ matrix
$Adim integer 1 number of positive eigen values of QAQ
$Ascores data.frame 9-8 Eigen vectors of QAQ '1/n' normed
$Aparam data.frame 8-3 Topological indices for nodes
$Bindica data.frame 9-8 class indicator from nodes
$Bscores data.frame 9-8 Topological orthonormal basis '1/n' normed
$Blabels character 8 Nodes labelling from orthonormal basis
>
> 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)) + } > > > >