I have been using the rescale function from geiger for a link prediction
model I recently helped develop (https://arxiv.org/abs/1707.08354). I'm now
running this model on a much larger dataset and part of the code is
computing cophenetic(rescale(phy)) with 'EB' rescaling many many times.

We're finding that calling cophenetic() is the rate limiting step, and if
we can avoid this function we expect to speed up our code by up to 4 times.
This would be very useful as our simulation has been running for over 50
days now...

I was wondering if there is a way to do EB transformations on a
phylogenetic distance matrix directly so as to avoid using the cophenetic

Any help or insights would be greatly appreciated!

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