Performance of Hamiltonian Monte Carlo and No-U-Turn Sampler for estimating genetic parameters and breeding values.

The No-U-Turn Sampler is a promising sampling method for animal breeding because of its good sampling qualities: large effective sample sizes, low autocorrelations, and low skewness of marginal posterior distributions, particularly when heritability is low. Meanwhile, Hamiltonian Monte Carlo failed to converge with a simple univariate model for pig data. Thus, it might be difficult to use Hamiltonian Monte Carlo for usual complex models in animal breeding.