Thanks again, that's very helpful and I'm going to try this out.
I have already tried a log10 transformation, and got a different error
message (using the latest version from github):
> bm_single = rateshift(tree, data, nrates=1)
Error in solve.default(sig * C + E) :
Lapack routine dgesv: system
Dear Lior.
> I don't know what property of my data creates this phenomenon. Could
> this be related to the very broad range of trait values (spanning two
> orders of magnitude)?
Based on the trait distribution, you might consider transforming your
data to a log-scale.
> 1. Is there a way to le
Hi Liam, and thanks a lot for the quick fix! I highly appreciate it.
I was able to install from github and the commands now completes
successfully. Unfortunately, convergence was not reached with 100
iterations. This is probably not surprising if the likelihood surface is
flat. I don't know what pr
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
t
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 opti
