read.tree.nodes: Read tree nodes

In lliu1871/phybase: Basic functions for phylogenetic analysis

Read tree nodes

Description

Read a tree string in parenthesic format and output tree nodes, species names and whether the tree is rooted

Usage

read.tree.nodes(str, name = "")

Arguments

str	a tree string in the parenthetical format
name	species names

Details

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 string and the first n nodes are in the same order as the species names appear in the tree string from left to right.

The numbers after ":" are branch lengths. The numbers after pound signs are population sizes. The numbers after "

Value

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.

Author(s)

Liang Liu [e-mail]

See Also

read.tree.string, species.name

Examples

##read an unrooted tree
data(dat.unrootedtree)
tree<-read.tree.nodes(dat.unrootedtree[1])
tree$nodes
tree$names
tree$root

#read a rooted tree
data(dat.coaltree)
tree<-read.tree.nodes(dat.coaltree$sptree)
tree$nodes
tree$names
tree$root

lliu1871/phybase documentation built on April 21, 2024, 3:16 a.m.