Ah, so while re-creating my problem for copy-paste-debug
goodness on the listserv, I discovered what was confusing me.
Originally, when I ran the various models, I got these
log-likelihoods for results:
==============================================
tf2ic2 kz kr turn
BM -9.923018 -9.725328 -9.740485 -44.67030
OU 17.939356 61.492326 43.530827 -42.22548
lambda -9.923018 -9.725328 -9.740485 -42.26222
kappa -9.923018 -9.725328 -9.740485 -44.45598
delta 18.121709 61.731899 42.452448 -43.09885
EB 9.649302 11.810710 11.612804 -44.67030
white 17.224360 58.832699 43.138356 -42.26222
==============================================
The trait data is roughly normal, the phylogeny is pretty
standard, so it was damned odd and rather hard to see why OU
and white noise (!) would be dozens of log-likelihood units
higher than Brownian motion, for instance. "turn" trait
data were all above 1, but for tf2ic2, kz, and kr, they were
below 1. So I was suspecting a bug or something.
As it turns out, back when first experimenting with
fitContinuous, I had input non-default bounds on the models,
and then forgot about it. I think I probably ruled some of
the optimal parameter values out-of-bounds for the trait
data <1, and this gave pathological results.
Going back to defaults, we get:
============================================
tf2ic2 kz kr turn
BM 17.46596 60.96182 40.75615 -44.67030
OU 17.93936 61.49233 43.53083 -42.22548
lambda 17.46596 60.96182 43.13836 -42.26235
kappa 17.46596 60.96182 41.43779 -44.45598
delta 18.12171 61.73190 42.45245 -43.09885
EB 17.46596 60.96182 40.75615 -44.67030
white 17.22436 58.83270 43.13836 -42.26222
============================================
...which seems far more reasonable...
Multiplying the trait data by 100 actually doesn't appear to
change the subsequent log-likelihoods in this case, in the
situation where the bounds are defaults rather than my
screwed-up bounds...
============================================
tf2ic2 kz kr turn
BM 17.46596 60.96182 40.75615 -44.67030
OU 17.93936 61.49233 43.53083 -42.22548
lambda 17.46596 60.96182 43.13836 -42.26235
kappa 17.46596 60.96182 41.43779 -44.45598
delta 18.12171 61.73190 42.45245 -43.09885
EB 17.46596 60.96182 40.75615 -44.67030
white 17.22436 58.83270 43.13836 -42.26222
============================================
...which is also encouraging.
So, basically, thanks for the help and sorry for the trouble!
Nick
On 3/7/11 4:41 PM, Dan Rabosky wrote:
Hi Nick-
Are you are getting differences in relative AICs between
models from simple rescaling (multiplying by a constant)?
The actual values of the traits *might* matter for
optimization, depending on various parameters associated
with optimization (and whatever algorithm is being used -
this should be L-BFGS-B for fitContinuous, I think). So...if
relative AICs are different, the first thing I would check
is whether some of your model AICs reflect local optima. Do
lots of optimizations with random starting parameters, which
is usually sufficient - and failing that, you can get into
the guts of optim and mess with the actual arguments that
control the optimization (e.g., parscale etc).
FYI, this is not immediately transparent in Geiger, as many
of the functions are hidden. To get at the optimization, look at
geiger:::fitContinuousModel
which does the heavy lifting within fitContinuous, and if
you need to, you can recode the relevant call to optim to
have a bit more flexibility.
~Dan
On Mar 7, 2011, at 4:04 PM, Nick Matzke wrote:
Doh! Really should have remembered that,
likelihoods-can-be-greater-than-1 is likelihood 101...
I am still a little puzzled by the dramatically different
results between rescaling and not, will try to post an
example in a sec...
--
====================================================
Nicholas J. Matzke
Ph.D. Candidate, Graduate Student Researcher
Huelsenbeck Lab
Center for Theoretical Evolutionary Genomics
4151 VLSB (Valley Life Sciences Building)
Department of Integrative Biology
University of California, Berkeley
Graduate Student Instructor, IB200B
Principles of Phylogenetics: Ecology and Evolution
http://ib.berkeley.edu/courses/ib200b/
http://phylo.wikidot.com/
Lab websites:
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http://fisher.berkeley.edu/cteg/hlab.html
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http://ib.berkeley.edu/people/students/person_detail.php?person=370
Lab personal page:
http://fisher.berkeley.edu/cteg/members/matzke.html
Lab phone: 510-643-6299
Dept. fax: 510-643-6264
Cell phone: 510-301-0179
Email: mat...@berkeley.edu
Mailing address:
Department of Integrative Biology
3060 VLSB #3140
Berkeley, CA 94720-3140
-----------------------------------------------------
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When people thought the earth was spherical, they were
wrong. But if you think that thinking the earth is spherical
is just as wrong as thinking the earth is flat, then your
view is wronger than both of them put together."
Isaac Asimov (1989). "The Relativity of Wrong." The
Skeptical Inquirer, 14(1), 35-44. Fall 1989.
http://chem.tufts.edu/AnswersInScience/RelativityofWrong.htm
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