subtree.test: Test the Yule or PDA hypothesis
In bcm-uga/apTreeshape: Analyses of Phylogenetic Treeshape

Description Usage Arguments Details Value Author(s) References See Also Examples

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.

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

`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"`.

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

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

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.

sackin.test
colless.test

## 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")