These functions print summaries of important HMC diagnostics.
The check_hmc_diagnostics
function calls the other functions internally
and prints an overall summary, but the other functions can also be called
directly:
check_divergences
prints the number (and percentage) of iterations that
ended with a divergence, check_treedepth
prints the number
(and percentage) of iterations that saturated the max treedepth,
and check_energy
prints E-BFMI values for each chain for which E-BFMI
is less than 0.2.
Brief explanations of some of the problems detected by these diagnostics can
be found at http://mc-stan.org/misc/warnings.html. For more depth see
Betancourt (2017).