is.clock: Is a clock tree or not

In lliu1871/phybase: Basic functions for phylogenetic analysis

Is a clock tree or not

Description

This function checks the tree to see if the branch lengths satisfy the molecular clock assumption. For each node, the lengths of the left lineage and right lineage are compared. If they are not equal to each other and the difference is greater than threshold, the function will return FALSE. This function does not perform statistical test for the molecular clock assumption.

Usage

is.clock(nodematrix, nspecies,threshold)

Arguments

nodematrix	the tree node matrix
nspecies	the number of species
threshold	the critical value for the difference between the length of the left decendant lineage and that of the right decendant lieage of an internode. The difference below the threshold is treated as no difference.

Value

The function returns TRUE for a clock tree and FALSE for a non-clock tree.

Author(s)

Liang Liu [e-mail]

See Also

is.rootedtree

Examples

treestr<-"((((H:0.00402,C:0.00402):0.00304,G:0.00705):0.00929,O:0.01635):0.1,W:0.11635);"
nodematrix<-read.tree.nodes(treestr)$nodes

##if the threshold is set to be large, the tree is a clock tree
is.clock(nodematrix,5,0.0001)
##[1] TRUE

##if the threshold is a small number, the tree is not a clock tree.
is.clock(nodematrix,5,0.00001)
##[1] FALSE

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