TRACER--Bayes factor

[Alice Yang]

Dear all:
When I calculated "Bayes Factor" using Tracer, It showed "ln Bayes
Factors"?

And then, I use the pull down menu to select any of the above(log10
Bayes Factors, ln Bayes Factors, Bayes Factors), but the numbers do
not change.
Could anybody tell me, what's problem?

Thanks

[mmateos]

I wasn't able to figure out what the Tracer Bayes Factors output was
really doing in terms of model comparison. I just use Tracer to
estimate the marginal posterior probabilities (no bootstrap); the
first column (the one that doesn't change when you change the log10
Bayes Factors, ln Bayes Factors, Bayes Factors). Then I calculate 2 x
the absolute difference between the marginal posterior probabilities
of two models, and use the Kass and Raftery table in Nylander et al.
2004 (Syst. Biol.) to make a decision.

Mariana

[Simon Ho]

Hi Alice,

The numbers should change if you change the option in the drop-down
menu.

In the Tracer window, make sure you select the log files for *all* of
the models you want to compare. Then the "Bayes Factors" window should
display a matrix containing all pairwise comparisons among the
candidate models. It is only these pairwise values (the Bayes factors)
that should change when the option in the drop-down menu is changed.

If you only select one model in the Tracer window when calculating
Bayes factors, the "Bayes Factors" window will only show the name of
the log file, the marginal likelihood, and the standard error. If this
is the case, changing the option in the drop-down menu will not affect
the values displayed.

Cheers,
Simon

[Maryam Zaman]

dear seniors, please tell me how should I calculate the Bayes factor in tracer? Ii will be thankful

[Guy Baele]

Calculating Bayes factors cannot be done in Tracer; instead, you should use Bayesian model selection through marginal likelihood estimation.
Tutorials can be found here:
http://beast.community/model_selection_1
http://beast.community/model_selection_2

Best regards,
Guy

 

Op dinsdag 28 april 2020 12:07:32 UTC+2 schreef Maryam Zaman:

[Maryam Zaman]

Thankyou  Guy.but one thing please guide.After beast run ends it shows me some warning can you please guide me about it.

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[Guy Baele]

Dear Maryam,

You can ignore that warning, it doesn't point to any problems.

Best regards,
Guy

Op maandag 4 mei 2020 12:43:49 UTC+2 schreef Maryam Zaman:

Thankyou  Guy.but one thing please guide.After beast run ends it shows me some warning can you please guide me about it.

On Wed, Apr 29, 2020 at 12:20 AM Guy Baele <bael...@gmail.com> wrote:

Calculating Bayes factors cannot be done in Tracer; instead, you should use Bayesian model selection through marginal likelihood estimation.
Tutorials can be found here:
http://beast.community/model_selection_1
http://beast.community/model_selection_2

Best regards,
Guy

 

Op dinsdag 28 april 2020 12:07:32 UTC+2 schreef Maryam Zaman:

dear seniors, please tell me how should I calculate the Bayes factor in tracer? Ii will be thankful

On Friday, March 18, 2011 at 10:56:42 AM UTC+5, Alice Yang wrote:

Dear all:
When I calculated "Bayes Factor" using Tracer, It showed "ln Bayes
Factors"?

And then, I use the pull down menu to select any of the above(log10
Bayes Factors, ln Bayes Factors, Bayes Factors), but the numbers do
not change.
Could anybody tell me, what's problem?

Thanks

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[Maryam Zaman]

Thankyou Guy.

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