which parameter affect ESS value?

[joey zhong]

hi,all
i am using Tracer to reconstruct Bayes skyline plot, but the most ESS
values are displayed in red, and lesser than 200.
so i wonder which parameter affect ESS value? and how to set to
make ESS value greater than 200?
thanks~

[Andrew Rambaut]

Dear Joey,

The only value that can reliably increase the ESS values is the MCMC chain length. That said, the Bayesian Skyline group sizes are integers and can be very auto-correlated because they don't change value much so I suggest you ignore low ESS values on these unless there is an obvious trend over time.

Andrew

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[Jean Mbisa]

Dear Andrew,
 
A related question to this.  What does the number of groups field stand for when you select Bayesian Skyline coalescent in BEAST? And how do you select the number of groups.  I have found that changes this number using my intrahost sequence data does influence the ESS values of the posterior, prior, likelihood and skyline.  Your help is greatly appreciated.

Regards,
Tamyo. 

 

> Subject: Re: which parameter affect ESS value?
> From: ram...@gmail.com
> Date: Tue, 22 May 2012 11:31:44 +0100
> To: beast...@googlegroups.com

[joey zhong]

Dear Andrew,

thanks for you great help.
using greater chain length, i found ESS values were better, but still
have many statistic items' ESS value in red.
i am raw hang in BEAST, wonder that how to get a reasonable skyline
plot, need all items' ESS values greater than 200?

thanks in advance for your help!

--joey