subtree.test {apTreeshape}R Documentation

Test the Yule or PDA hypothesis

Description

subtree.test tests the likelihood of the Yule or the PDA hypothesis and computes the p-value of the test. The test is based on the number of subtrees of a given size in the tree.

Usage

subtree.test(tree, size , alternative = "two.sided")

Arguments

tree

An object of class "treeshape".

size

The size of the subtrees to test for.

alternative

The alternative hypothesis of the test. It can be "two.sided" (default), "less" or "greater".

Details

See references for the mathematical details of the test. It uses a Gaussian approximation to compute the p-value.

Value

A list containing the following arguments :

statistic

the value of the statistic used in the test

p.value

the p-value of the test

alternative

the alternative hypothesis used for the test

Author(s)

Michael Blum <michael.blum@imag.fr>
Nicolas Bortolussi <nicolas.bortolussi@imag.fr>
Eric Durand <eric.durand@imag.fr>
Olivier Francois <olivier.francois@imag.fr>

References

Blum, Michael GB, and Olivier Francois. Minimal clade size and external branch length under the neutral coalescent. Advances in Applied Probability 37.3 (2005): 647-662.

See Also

sackin.test
colless.test

Examples


## Generate a random pda tree with 50 tips
tr<-rtreeshape(n=1,tip.number=50,model="pda")
tr<-tr[[1]]

## Test the yule hypothesis, using subtrees of size 2 (Cherries), 
##      with the alternative hypothesis "less"
subtree.test(tr,size=2,alternative="less")

[Package apTreeshape version 1.5-0.1 Index]