I'm trying to use chronos (ape version 5.2) to scale a tree of ~800 tips, with
branch lengths derived from a RAxML analysis. I'm using 4 outgroup
calibrations. When I run the analysis using
t.og <- chronos(tree, lambda = 1, model = "relaxed", quiet = FALSE,
calibration = dd.out)
I get the following returned, in almost 5 seconds:
Setting initial dates...
Fitting in progress... get a first set of estimates
Penalised log-lik = -1e+100
Optimising rates... dates... -1e+100
Done.
a look at attributes (attr(t.og, "message")) gives a "relative convergence
(4)." The pLL, however, is -Inf. I have tried setting chronos.control to
different values, with no success. It looks like it may be an issue with the
optimization function inside chronos.
Are there additional constraints/code I can apply to make it optimize without
(apparently) simply running to the boundary?
Thanks,
~John
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