Could anyone kindly let me know where the source codes of NUTS are stored for Stan? I found some folders in Github for C++ and MatLab. However, I am not sure which folders are the “offiical” ones for the Rstan package.
I am trying to figure out the details of the algorithm NUTS in the codes. Thank you for your help in advance.
Although Stan (Stan Development Team, 2017) was first developed around this original No-U-Turn sampler, more recent releases have adopted some modifications. In addition to the generalized No-U-Turn termination criterion, the Hamiltonian Monte Carlo implemen- tation in Stan uses multinomial sampling from each trajectory instead of slice sampling, which provides a significant improvement in overall performance.
Thank you for your clarification. I will read both of them in details. I read the first paper before but not the second one. There are so many small C++ codes for NUTS in Github, including NUTS, NUTS_classic, etc. I was a little bit lost. Your explanations help to explain them now.