Using BEAST2 fossilized birth death model, I'm receiving low/red ESS values specifically for my posterior and prior. I'm already at 100M generations, which seems really high, but aside from increasing the generation number more, how do I increase the ESS values?
Hi Dalton,
Actually, 100M generations is really high. I guess the problem is more related with the prior, maybe your prior assumptions are not the correct ones. The prior represents your prior belief or prior assumptions about the probabilities of different parameter values before you have analyzed the data. Moreover, the prior is combined with the likelihood to yield the posterior, that´s why also your posterior EES value is low.
Best wishes
David
Besides the potential prior issue as David pointed out, one can also increase the "thinning" parameter to decrease the auto-correlation between the samples. E.g., if thinning is 5, the sample will then use every 5th sample of the mcmc chain, in other words, 1st, 6th, 11st, 16th, etc.
I have maximized most of the scales at the operators tab, and my ESS significantly increased, will that have an effect on my analysis?
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