README

Programs (in R) for the results in the paper:

  Modifying Gibbs Sampling to Avoid Self Transitions
  Radford M. Neal, 2024

The paper is in gibbs-self.pdf here, and at https://arxiv.org/abs/2403.18054

The algorithms described in the paper are implemented (in R) in the
file methods.r.  Various checks for validity of these methods are
done in check-all.r.

The experimental runs reported in the paper can be reproduced with the
run-potts-8x8, run-potts-5x5, run-mix, run-beliefnet, and run-other
shell scripts.  These runs take a long time - several days, in total.
The outputs of these runs are in the sub-directory 'runs', except for
the saved R workspaces, which would be quite large.

Checking out the small-runs branch of this repository will switch to
smaller runs (1/100 the length of the full runs), which take only
about a half hour or less for each shell script.  Of course, the
asymptotic variance estimates are then much noisier.  The results of
these smaller runs are in the 'runs' sub-directory when the small-runs
branch is checked out.