In the package phylolm, the function "transf.branch.lengths” might do what you
need. It has an option model=“EB” for early burst.
> On Dec 15, 2017, at 3:27 PM, Max Farrell <maxwellfarr...@gmail.com> wrote:
> 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!
> [[alternative HTML version deleted]]
> R-sig-phylo mailing list - Rfirstname.lastname@example.org
> Searchable archive at http://email@example.com/
R-sig-phylo mailing list - Rfirstname.lastname@example.org
Searchable archive at http://email@example.com/