| 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 |
... |
: 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 |
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
S?bastien Ollier sebastien.ollier@u-psud.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(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))
}