Re: [R-sig-phylo] extracting from mrbayes

[David Bapst]

John,

I had to double-check this with someone who knew better first, but
they confirmed for me that the answer is that MrBayes doesn't infer a
Q matrix. By default, the Q matrix for Mk in MrBayes is always held
fixed so the rates of transition are always equal and fully
reversible, i.e. a simple Jukes-Cantor model. There's no setting that
allows MrBayes to freely vary and infer a Q matrix, but you can relax
the assumption of symmetrry via the symmetric Dirichlet hyperprior. If
you want to infer a Q model under a different model, there are lots of
R functions for fitting models to discrete character data, such as in
geiger or ape.

I suggest seeing April Wright et al.'s recent paper in Systematic
Biology for a clear explanation of this:.
http://sysbio.oxfordjournals.org/content/65/4/602

I hope this helps!

Cheers,
-Dave Bapst



On Tue, Jul 19, 2016 at 3:15 PM, John Denton  wrote:
> Hi folks,
>
> I need to do some simulation using the Mkv model, and am wondering if there 
> is a way to extract Mk Q-matrix values from mrbayes. A look at report lists 
> revmat as an output, but I do not see any parameters in the .p files when I 
> finish the run.
>
> Thanks,
>
> ~John
>
>
> John S. S. Denton, Ph.D.
> Department of Vertebrate Paleontology
> American Museum of Natural History
> www.johnssdenton.com
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> R-sig-phylo mailing list - R-sig-phylo@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
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-- 
David W. Bapst, PhD
Adjunct Asst. Professor, Geology and Geol. Eng.
South Dakota School of Mines and Technology
501 E. St. Joseph
Rapid City, SD 57701

http://webpages.sdsmt.edu/~dbapst/
http://cran.r-project.org/web/packages/paleotree/index.html

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[R-sig-phylo] extracting from mrbayes

[John Denton]

Hi folks,

I need to do some simulation using the Mkv model, and am wondering if there is 
a way to extract Mk Q-matrix values from mrbayes. A look at report lists revmat 
as an output, but I do not see any parameters in the .p files when I finish the 
run.

Thanks,

~John


John S. S. Denton, Ph.D.
Department of Vertebrate Paleontology
American Museum of Natural History
www.johnssdenton.com
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