I wonder if there’s a clean way to calculate IAT from the Stan output. The documentation on LaplaceDeamon says
The
IAT
of a continuous chain correlates with the variability of the mean of the chain and relates to Effective Sample Size (ESS
) and Monte Carlo Standard Error (MCSE
).IAT
andESS
are inversely related, though not perfectly because each is estimated a little differently. GivenNN
samples and taking autocorrelation into account,ESS
estimates a reduced number ofMM
samples. Conversely,IAT
estimates the number of autocorrelated samples, on average, required to produce one independently drawn sample.
I came across the Sokal (1997) reference, but could not see how to relate his definition of IAT with the ESS/MCSE measures available in posterior::summary(). I understand that this is something that is only meaningful per chain.
References:
Sokal, A. (1997). Monte Carlo Methods in Statistical Mechanics: Foundations and New Algorithms. NATO ASI Series, 131–192. doi:10.1007/978-1-4899-0319-8_6