StatSVN - Directory src/dr/inference/ml/

Lines of Code

src/dr/inference/ml/ Lines of Code

Developers

Author	Changes	Lines of Code	Lines per Change
Totals	10 (100.0%)	33 (100.0%)	3.3
jheled	4 (40.0%)	24 (72.7%)	6.0
rambaut	5 (50.0%)	9 (27.3%)	1.8
dong.w.xie	1 (10.0%)	0 (0.0%)	0.0

Most Recent Commits

rambaut 2011-11-15 09:26 Rev.: 4424

Upgraded chain length to a 64 bit integer so that chain lengths > 2.1 billion can be done. This addresses issue 540. Runs OK, accepts long chain lengths but not actually tested a run of > 2.1 billion.

6 lines of code changed in 2 files:

src/dr/inference/ml: MLOptimizer.java (+6 -6)

dong.w.xie 2010-03-02 10:05 Rev.: 3001

Trunk refactoring: finish MCMC (split parsers).

0 lines of code changed in 1 file:

src/dr/inference/ml: MLOptimizer.java (-61)

rambaut 2009-10-03 00:23 Rev.: 2341

Replaced 'preBurnin' with an autoOptimizeDelay (coercionDelay). The rationale for this is that the preBurnin meant that the initial state was not in the log files, it was unecessary and it cause a small inefficiency as the JIT compiler re-optimized after the preburnin chain had finished. We also didn't see warning messages until after the pre-burnin period. There is a new attribute to the MCMC parser - autoOptimizeDelay (to which the old preBurnin attribute now maps so old XML will run).

1 lines of code changed in 1 file:

src/dr/inference/ml: MLOptimizer.java (+1 -1)

jheled 2009-07-15 13:44 Rev.: 1858

comment out operator experimental code

6 lines of code changed in 1 file:

src/dr/inference/ml: MLOptimizer.java (+6 -6)

jheled 2009-05-16 13:05 Rev.: 1719

Control number of operator evaluation checks via minOpsFullEvaluations.

Add 'minOpsFullEvaluations="0" fullEvaluation="0"' to the <mcmc> attributes to disable checks altogether.

1 lines of code changed in 1 file:

src/dr/inference/ml: MLOptimizer.java (+1 -1)

rambaut 2009-04-14 06:44 Rev.: 1568

Broke the build with my last clean up (removing a hack in MarkovChain). Sorry.

1 lines of code changed in 1 file:

src/dr/inference/ml: MLOptimizer.java (+1 -1)

jheled 2008-04-27 17:42 Rev.: 832

experimental on-the-fly updating of operator weights with -otfops. Absolutly no guarantee - may make things worse

1 lines of code changed in 1 file:

src/dr/inference/ml: MLOptimizer.java (+1 -1)

rambaut 2007-07-10 20:52 Rev.: 379

Have made 'fullEvaluationCount' an attribute of MCMC. If not specified then it has a default of 2000 (this is now an option in MCMCOptions). Set to chain length to fully evaluate the likelihood after every restore.

1 lines of code changed in 1 file:

src/dr/inference/ml: MLOptimizer.java (+1 -1)

jheled 2007-06-25 11:20 Rev.: 320

generify & simplify

16 lines of code changed in 1 file:

src/dr/inference/ml: MLOptimizer.java (+16 -25)