NOTES ON THE VERSION OF 1999-12-06

This is a fairly minor release, with a few bug fixes, a couple of
which might be important, some new experimental facilities that aren't
of general interest (at least not yet), and a few added conveniences
and other minor updates.


Changes in this version:

1) Several new ways of computing trajectories have been implemented,
   in addition to the old leapfrog method.  See mc-spec.doc for details.
   The new methods may be better for some applications, but they aren't
   uniformly better than the leapfrog method, and they are not recommended
   for general use.

2) New "spiral" and "double-spiral" operations were added.  See 
   mc-spec.doc for details.  These are experimental.  Quantities
   m0, m1, m2, m3, m4, and m5 were added to support this feature.  
   See mc-quantities.doc for details.

3) The mc-spec program now lets you see all the specifications in 
   the log file, at any iteration, with "mc-spec log-file all".  See 
   mc-spec.doc for details.

4) New "multiply-momentum" and "set-momentum" operations were added, for
   testing and research purposes.  See mc-spec.doc for details.  These
   are probably of no interest to most users.

5) An install-arch shell file for conveniently maintaining separate
   versions of the compiled programs for different machine architectures
   has been added.

6) The documentation has been updated and corrected in various fairly
   minor ways.

7) Compute times quoted for the demos are now for a Linux system with
   a 550MHz Pentium III processor.


Bug fixes.

1) A bug was fixed that caused derivatives to sometimes be calculated 
   incorrectly when the "omit" option was used with Gaussian process
   models.  The effect was to increase the rejection rate for "hybrid"
   operations, but the final answer (if convergence was reached) would 
   still be correct.

2) A bug was fixed that caused the "first:last" option of the met-1
   operation to be ignored.

3) A bug was fixed that sometime caused data-spec to report spurious
   errors when targets were log-transformed.

4) A bug was fixed that caused problems with automatic scaling of target
   variables when they were all the same (ie, had standard deviation of 0).

5) The xxx-stepsizes and xxx-grad-test programs were changed to not try
   to open the log file for writing (which might not be allowed), seeing
   as they only need to read it.


Known bugs and other deficiencies.

1) The facility for plotting quantities using "plot" operations in xxx-mc
   doesn't always work for the first run of xxx-mc (before any
   iterations exist in the log file).  A work-around is to do a run of
   xxx-mc to produce just one iteration before attempting a run of
   xxx-mc that does any "plot" operations.

2) The CPU time features (eg, the "k" quantity) will not work correctly
   if a single iteration takes more than about 71 minutes.

3) The latent value update operations for Gaussian processes may recompute 
   the inverse covariance matrix even when an up-to-date version was 
   computed for the previous Monte Carlo operation.

4) Covariance matrices are stored in full, even though they are symmetric,
   which sometimes costs a factor of two in memory usage.

5) The "p" option of net-pred isn't allowed for survival models with
   piecewise-constant hazard.  There's no big reason for this - I just
   haven't gotten around to it.