treeGrowth_eu

Important notes for diagnosis

Source: https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup

1. Specifically for low BFMI warnings:
   • Look at the pairs plot to see which primitive parameters are correlated with the energy__ margin.
   • The primitive parameters that are correlated with the energy__ margin in the pairs plot are a good place to start thinking about reparameterizations. There should be be a negative relationship between lp__ and energy__ in the pairs plot, but this is not a concern because lp__ is the logarithm of the posterior kernel rather than a primitive parameter.
2. Specifically for Rhat, ESS, low BFMI warnings: You might try setting a higher number of warmup or sampling iterations. Increasing the number of iterations is rarely helpful for resolving divergences/max treedepth warnings.
   • Look at change in bulk-ESS and tail-ESS when the number of iterations increase. If R-hat is less than 1.01 and ESS grows linearly with the number of iterations and eventually exceeds the recommended limit, the mixing is sufficient but MCMC has high autocorrelation requiring a large number of iterations.

Run order for scripts

1. prepare_growth_data.R