khabbazian / l1ou

Detection of evolutionary shifts in Ornstein-Uhlenbeck models
GNU General Public License v2.0
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Hello Mohammad, I have removed normalized tree from 2 R files and checks the package works fine #21

Closed yuqing19118 closed 7 years ago

cecileane commented 7 years ago

@yuqing19118, based on @khabbazian's comment here, I think that the division by 2*α should be made earlier on the branches of the tree, instead of later on the 2 matrices (square-root and inverse square-root). If small α values caused huge branch lengths and numerical errors due to a tiny inverse square-root matrix, it's best to rescale the branch lengths first, than to allow for huge branch lengths, run the square-root matrix calculation on them, and rescale the 2 matrices (one huge, one tiny) at the end.

I think that we should make this other change before a pull request. Advice welcome Mohammad!