StatSVN - Directory src/dr/inference/mcmcmc/

Lines of Code

src/dr/inference/mcmcmc/ Lines of Code

Developers

Author	Changes	Lines of Code	Lines per Change
Totals	17 (100.0%)	265 (100.0%)	15.5
rambaut	12 (70.6%)	151 (57.0%)	12.5
alexei.drummond	2 (11.8%)	104 (39.2%)	52.0
jheled	3 (17.6%)	10 (3.8%)	3.3

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.

15 lines of code changed in 4 files:

src/dr/inference/mcmcmc: MCMCMC.java (new), MCMCMCRunner.java (new)

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).

2 lines of code changed in 2 files:

src/dr/inference/mcmcmc: MCMCMC.java (+1 -1), MCMCMCRunner.java (+1 -1)

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

comment out operator experimental code

1 lines of code changed in 1 file:

src/dr/inference/mcmcmc: MCMCMCRunner.java (+1 -1)

jheled 2009-07-15 13:44 Rev.: 1857

automatic intelliJ stuff

8 lines of code changed in 1 file:

src/dr/inference/mcmcmc: MCMCMC.java (+8 -7)

rambaut 2009-04-14 09:01 Rev.: 1569

Added a getCount to the operator interface and a getMinimumCount to OperatorSchedule. This gives the number of times the least frequently used operator has been called.

6 lines of code changed in 1 file:

src/dr/inference/mcmcmc: MCMCMC.java (+6 -6)

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/mcmcmc: MCMCMCRunner.java (+1 -1)

alexei.drummond 2008-07-22 22:05 Rev.: 1002

renamed mispelled method (setSumDeviation), added CoercionMode enum and refactored autoOptimize parsing accordingly. Added ability to log to memory and import newick from string.

8 lines of code changed in 1 file:

src/dr/inference/mcmcmc: MCMCMC.java (+8 -6)

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/mcmcmc: MCMCMCRunner.java (+1 -3)

rambaut 2008-01-09 12:21 Rev.: 652

Various improvements to BEAUti and the odd bit of cleaning up. Some additions to tracer

7 lines of code changed in 2 files:

src/dr/inference/mcmcmc: MCMCMC.java (+3 -4), MCMCMCRunner.java (+4 -1)

alexei.drummond 2007-08-08 21:50 Rev.: 469

tidying

96 lines of code changed in 1 file:

src/dr/inference/mcmcmc: MCMCMC.java (+96 -56)

rambaut 2007-07-26 21:28 Rev.: 429

Fixed problem logging trees MCMCMC (was giving null taxon labels).

9 lines of code changed in 1 file:

src/dr/inference/mcmcmc: MCMCMC.java (+9 -11)

rambaut 2007-07-19 23:12 Rev.: 412

Possibly fixed problem with swapping loggers during MCMCMC. This compiles but is not tested - have run out of time.

111 lines of code changed in 1 file:

src/dr/inference/mcmcmc: MCMCMC.java (+111 -102)