read.tree.nodes {phybase} | R Documentation |
Read a tree string in parenthesic format and output tree nodes, species names and whether the tree is rooted
read.tree.nodes(str, name = "")
str |
a tree string in the parenthetical format |
name |
species names |
This function reads a tree string into a matrix that describes the relationships among nodes and corresponding branch lengths. Each row in the matrix represents a node. The first n rows contain the information of the nodes at the tips of the tree. The order of the first n nodes is identical to the alphabetic order of the species names given by {name}. If {name} is null, the names will be extracted from the tree {str} and the first n nodes are in the same order as the species names appear in the tree {str} from left to right.
The numbers after ":" are branch lengths. The numbers after pound signs are population sizes. The numbers after "
nodes |
nodes is a matrix that describes the relationships among nodes and corresponding branch lengths and population sizes if the tree is a species tree. Each row corresponds a node in the tree. The matrix has 5 columns. The first column is the father of the current node. The following columns are left son, right son, branch length, and population size. The value -9 implies that the information does not exist. The last row is the root of the tree. If the tree is unrooted, the first number of the root node is -8, while it is -9 for a rooted tree. |
names |
species names in the same order of the first n nodes. |
root |
TRUE for a rooted tree, FALSE for an unrooted tree. |
Liang Liu lliu@oeb.harvard.edu
read.tree.string
, species.name
##read an unrooted tree data(unrooted.tree) tree<-read.tree.nodes(unrooted.tree[1]) tree$nodes tree$names tree$root #read a rooted tree data(rooted.tree) tree<-read.tree.nodes(rooted.tree[1]) tree$nodes tree$names tree$root