Re: [migrate-support] Cannot run heated chains

[Peter Beerli]

On Apr 28, 2013, at 3:17 AM, 9ian <shen...@gmail.com> wrote:

Hi Peter,

Every time I try to run heated chains (because calculating Bayes Factor requires heating), Migrate-n sticks there and cannot start sampling (see screenshot). I have already set a small sample numbers and built-ins. I am using microsatellite data (6 populations, 5 loci, a total of 180 sampled individuals). I use 4 static chains with 10 interval and an "#" option. Previously found prior for theta and M during test run are: Theta{0, 20, 0.05} M{0, 50, 0.5}. Is there anything I missed?

Thanks and looking forward to the reply.

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<キャプチャ.PNG>

[Peter Beerli]

On Apr 28, 2013, at 3:56 AM, 9ian <shen...@gmail.com> wrote:

Hello,

Figured out by myself after searching for a number of papers: microsatellite data under Brownian motion mutation model can run heated chains. But why stepwise mutation model doesn't work?

[Peter Beerli]

The microsatellite model should work fine but it takes incredibly much longer on large datasets, I suggest that you stick to the brownian motion model

Peter

[Peter Beerli]

Qian,

eventually there will be all figures in the handouts, every time I teach this class more figures are added to the handout, but maybe the figures are there if you look at the newer version at

http://people.sc.fsu.edu/%7Epbeerli/classes/ISC5317/ISC5317/Main.html

Peter

On Apr 29, 2013, at 1:00 AM, 9ian <shen...@gmail.com> wrote:

Hi Peter,

Thanks very much for the reply! BTW, I found one of your lecture notes explaning mutation models (http://people.sc.fsu.edu/~pbeerli/BSC-5936/09-19-05/mutation-model-III.pdf), but some figures are missing in this PDF file. It would be a good learning material so any ideas on an updated version of this short but informative lecture note?

 

Best.

 

Qian