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 |
size |
The size of the subtrees to test for. |
alternative |
The alternative hypothesis of the test. It can be |
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.
1 2 3 4 5 6 7 | ## 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")
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