Hello,
I am trying to run the rateshift function from phytools on a rather large
phylogeny (500 species).
With nrates=1 (null model) everything works fine. Using nrates=2 also
completed successfully, but did not reach convergence:
> bm_multi = rateshift(tree, data, nrates=2)
> bm_multi$convergence
Hi Lior.
I'm working on this for you now.
Basically a lot of optimization iterations with /rateshift/ tend to
fail, so I'm basically doing two things: (1) preventing a failed
optimization from causing the whole run to fail using /try/; and (2)
allowing the user to parallelize the multiple
Hi Lior.
I just updated /rateshift/ in /phytools/ on GitHub with these
adjustments. It seems to work well and will run your dataset without
failing.
I did observe an odd thing with the two-rate model for your data which
is that the likelihood surface for the position of the rate-shift seems
