Thanks for the input - it looks like this function does perform the tree
rescaling, and in about 1/4 of the time, so this could help speed up the
However, the function doesn't seem to return a covariance matrix. Is there
a way to get the cophenetic matrix with the out put of this function?
Otherwise I'm stuck using cophenetic again...
On Fri, Dec 15, 2017 at 4:36 PM, Cecile Ane <cecile....@wisc.edu> wrote:
> 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>
> > 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
> > 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
> > 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
> > function?
> > Any help or insights would be greatly appreciated!
> > [[alternative HTML version deleted]]
> > _______________________________________________
> > R-sig-phylo mailing list - Remail@example.com
> > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> > Searchable archive at http://www.mail-archive.com/r-
> R-sig-phylo mailing list - Rfirstname.lastname@example.org
> Searchable archive at http://www.mail-archive.com/r-
[[alternative HTML version deleted]]
R-sig-phylo mailing list - Remail@example.com
Searchable archive at http://firstname.lastname@example.org/