tree.partition: partition a tree

In lliu1871/phybase: Basic functions for phylogenetic analysis

partition a tree

Description

partition a tree.

Usage

tree.partition(tree,nspecies)

Arguments

tree	the tree node matrix
nspecies	the number of species

Value

The function returns a matrix. Each row represents a particular partition of the tree. The position of "1" in the matrix indicates the presence of the corresponding species in the partition. The last number at each row is the frequency of that partition. This function returns the partition matrix for only one tree.

Author(s)

Liang Liu

Examples

treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00707):0.00929,O:0.01635):0.1,W:0.12);"
nodematrix<-read.tree.nodes(treestr)$nodes
tree.partition(nodematrix,5)
#
#     [,1] [,2] [,3] [,4] [,5] [,6]
#[1,]    1    0    1    0    0    1
#[2,]    1    1    1    0    0    1
#[3,]    1    1    1    1    0    1
#
#The last number of each row is the frequency of the corresponding partition. 
#For example, the frequency of the first partition (1 0 1 0 0) is 1. 
#The first partition includes species 1 and 3 
#as indicated by the position of 1 in the partition. 
#Each row represens a partition and its frequency.

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