tree utility function
Functions for describing relationships among phylogenetic nodes.
Ancestors(x, node, type = c("all", "parent"))
allDescendants(x)
Children(x, node)
Descendants(x, node, type = c("tips", "children", "all"))
Siblings(x, node, include.self = FALSE)
mrca.phylo(x, node = NULL, full = FALSE)x |
a tree (a phylo object). |
node |
an integer or a vector of integers corresponding to a node ID |
type |
specify whether to return just direct children / parents or all |
include.self |
whether to include self in list of siblings |
full |
a logical indicating whether to return the MRCAs among all tips and nodes (if TRUE); the default is to return only the MRCAs among tips. |
These functions are inspired by treewalk in phylobase package, but
work on the S3 phylo objects. The nodes are the indices as given in
edge matrix of an phylo object. From taxon labels these indices can be
easily derived matching against the tip.label argument of an phylo
object, see example below. All the functions allow node to be either
a scalar or vector. mrca is a faster version of the mrca in ape, in
phangorn only because of dependencies.
If the argument node is missing the function is evaluated for all nodes.
a vector or a list containing the indices of the nodes.
allDescendants: list all the descendant nodes of each node
treewalk, as.phylo,
nodelabels
tree <- rtree(10)
plot(tree, show.tip.label = FALSE)
nodelabels()
tiplabels()
Ancestors(tree, 1:3, "all")
Children(tree, 11)
Descendants(tree, 11, "tips")
Siblings(tree, 3)
# Siblings of all nodes
Siblings(tree)
mrca.phylo(tree, 1:3)
mrca.phylo(tree, match(c("t1", "t2", "t3"), tree$tip))
mrca.phylo(tree)
# same as mrca(tree), but faster for large treesPlease choose more modern alternatives, such as Google Chrome or Mozilla Firefox.