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I am currently trying to use MCMC technqiues to produce mean estimates of animal tracking locations. I am using JAGS (Just Another Gibbs Sampler) in R. Now, I am trying to find out what the most suitable parameters for nr. iterations after the burn-in, burn-in and thinning intervals are.

My idea is to use the Rafter Lewis diagnostic with the raftery.diag() function from the package "coda". However, I am a bit confused about the output. According to the documentation, the output of the function contains a 3d array with M = suggested burn-in, N = suggested number of iterations and Nmin = suggested number of iterations based on zero autocorrelation.

My two questions are:

What does "Error" "3746" in the resmatrix mean and how can I solve this error?

How can I find the suggested thinning interval in the raftery.diag() output?

vheim
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  • You will be most likely to get your question answered if you follow the [helpful advice](https://stackoverflow.com/help/how-to-ask) about asking questions and create a [reproducible example](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example). – DaveArmstrong Jan 14 '22 at 16:35

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