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baele.guy@gmail.com 2013-02-21 22:38 Rev.: 5448

Fixed citation error.

1 lines of code changed in 2 files:

• src/dr/inference/mcmc: MarginalLikelihoodEstimator.java (new)

baele.guy@gmail.com 2013-02-07 02:28 Rev.: 5381

Operator reporting and citation fix.

5 lines of code changed in 1 file:

• src/dr/inference/mcmc: MarginalLikelihoodEstimator.java (+5 -1)

baele.guy@gmail.com 2013-01-29 02:19 Rev.: 5345

bug fix

1 lines of code changed in 1 file:

• src/dr/inference/mcmc: MarginalLikelihoodEstimator.java (+1 -1)

baele.guy@gmail.com 2012-12-08 23:21 Rev.: 5281

Small correction in keeping track of the number of steps.

3 lines of code changed in 1 file:

• src/dr/inference/mcmc: MarginalLikelihoodEstimator.java (+3 -2)

msuchard 2012-12-04 08:11 Rev.: 5272

Updated PrecisionMatrixGibbsOperator for functionality within path sampling from posterior to prior. Should still cause errors in path sampling between two arbitrary models.

12 lines of code changed in 1 file:

• src/dr/inference/mcmc: MarginalLikelihoodEstimator.java (+12 -8)

alexander.alekseyenko 2012-11-20 11:02 Rev.: 5245

resolving Issue 630.

3 lines of code changed in 1 file:

• src/dr/inference/mcmc: MarginalLikelihoodEstimator.java (+3 -3)

Sibon.Li@gmail.com 2012-09-18 19:14 Rev.: 5170

Changes to MarkovChainDelegate to allow it better access and privileges to MarkovChain

1 lines of code changed in 2 files:

• src/dr/inference/mcmc: MCMC.java (new)

rambaut 2012-08-16 03:27 Rev.: 5136

Porting r5135 from 1.7 branch

0 lines of code changed in 1 file:

• src/dr/inference/mcmc: MCMC.java (-8)

rambaut 2012-08-11 08:53 Rev.: 5122

Fix for Issue 655: Operator log sometimes attempts to write to locked folder causing exception. Needs testing and porting to 1.7 branch.

8 lines of code changed in 1 file:

• src/dr/inference/mcmc: MCMC.java (+8 -9)

baele.guy@gmail.com 2012-06-08 20:18 Rev.: 5025

Added the possibility to run a power posterior for a single fixed power.

34 lines of code changed in 1 file:

• src/dr/inference/mcmc: MarginalLikelihoodEstimator.java (+34 -2)

baele.guy@gmail.com 2012-05-25 00:56 Rev.: 5002

Bugfix for the linear integrator scheme.

3 lines of code changed in 1 file:

• src/dr/inference/mcmc: MarginalLikelihoodEstimator.java (+3 -2)

baele.guy@gmail.com 2012-05-24 22:31 Rev.: 4999

Minor change to text output.

5 lines of code changed in 1 file:

• src/dr/inference/mcmc: MarginalLikelihoodEstimator.java (+5 -5)

sibon.li 2012-04-07 06:46 Rev.: 4920

Added an interface for delegating tasks in the Markov Chain

55 lines of code changed in 1 file:

• src/dr/inference/mcmc: MCMC.java (+55 -1)

baele.guy@gmail.com 2012-03-23 21:55 Rev.: 4880

Bug fix for beta quantile integrator scheme.

5 lines of code changed in 1 file:

• src/dr/inference/mcmc: MarginalLikelihoodEstimator.java (+5 -1)

rambaut 2012-03-04 01:01 Rev.: 4761

Removing wrongly located files.

0 lines of code changed in 1 file:

• src/dr/inference/mcmc: BlueBeastMCMC.java (del)

sibon.li 2012-03-03 21:38 Rev.: 4758

Commented out all of my last commit until issues resolved

199 lines of code changed in 1 file:

• src/dr/inference/mcmc: BlueBeastMCMC.java (new 199)

sibon.li 2012-03-03 16:23 Rev.: 4755

Added classes to enable implicit convergence assessment checks using BLUE

200 lines of code changed in 1 file:

• src/dr/inference/mcmc: BlueBeastMCMC.java (+200)

sibon.li 2012-03-03 16:18 Rev.: 4754

Changes to encapsulation in MCMC.java and MarkovChain.java. MarkovChain.java no longer final and some private variables changed to protected

13 lines of code changed in 1 file:

• src/dr/inference/mcmc: MCMC.java (+13 -13)

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.

27 lines of code changed in 4 files:

• src/dr/inference/mcmc: MCMC.java (+8 -8), MCMCOptions.java (+3 -3), MarginalLikelihoodEstimator.java (+16 -16)

rambaut 2011-07-28 04:08 Rev.: 4128

Addressed issue 472: http://code.google.com/p/beast-mcmc/issues/detail?id=472

Doesn't show operator performance suggestion when auto-optimize is on.

11 lines of code changed in 1 file:

• src/dr/inference/mcmc: MCMC.java (+11 -9)

baele.guy@gmail.com 2011-06-10 07:17 Rev.: 4023

Added a SigmoidIntegrator which allows taking small sampling steps towards the edges of the integration interval (see Lepage et al., 2007). An example of how to use this new integrator was added to examples/release/testTreePathSampling.xml.

32 lines of code changed in 1 file:

• src/dr/inference/mcmc: MarginalLikelihoodEstimator.java (+32 -1)

baele.guy@gmail.com 2011-06-09 04:29 Rev.: 4019

Added a "beta quantile integrator" (see Xie et al., 2010 and Fan et al., 2011) as an alternative path scheme for the beta values in the thermodynamic integration framework. See examples/release/testTreePathSampling.xml for an example on how to use this integrator.

22 lines of code changed in 1 file:

• src/dr/inference/mcmc: MarginalLikelihoodEstimator.java (+22 -1)

baele.guy@gmail.com 2011-06-08 22:24 Rev.: 4017

Placed two unused (deprecated) methods into comment

19 lines of code changed in 1 file:

• src/dr/inference/mcmc: MarginalLikelihoodEstimator.java (+19 -18)

baele.guy@gmail.com 2011-06-06 21:23 Rev.: 4013

Small correction to the GeometricIntegrator

1 lines of code changed in 1 file:

• src/dr/inference/mcmc: MarginalLikelihoodEstimator.java (+1 -1)

rambaut 2010-06-12 03:51 Rev.: 3252

Prettied-up the printing of diagnostic message for a zero initial likelihood (actually this is a port of a improvement from the BEAST v1.5.x branch).

1 lines of code changed in 1 file:

• src/dr/inference/mcmc: MCMC.java (+1 -1)

rambaut 2010-06-07 23:59 Rev.: 3236

Normalized the naming of a few classes and added a note in the MCMC parser to say if the fullEvaluation has been turned off.

1 lines of code changed in 1 file:

• src/dr/inference/mcmc: MCMCOptions.java (+1 -1)

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/mcmc: MCMCParser.java (del)

dong.w.xie 2010-02-03 10:11 Rev.: 2876

Trunk: hide the confused constructor from MCMC.

25 lines of code changed in 2 files:

• src/dr/inference/mcmc: MCMC.java (+23), MCMCParser.java (new 2)

alexander.alekseyenko 2010-01-29 07:44 Rev.: 2853

Fixed burn-in issues in MLE, restructured integration procedure, now using Integrator classes for handling different integration schemes.

129 lines of code changed in 1 file:

• src/dr/inference/mcmc: MarginalLikelihoodEstimator.java (+129 -111)

alexander.alekseyenko 2010-01-17 10:15 Rev.: 2811

Minor changes to Path Sampling Marginal Likelihood Estimation and Bayes Factor analysis, including:
- Operator analysis printer class (general purpose);
- Operator schedule, critical bug fix;
- Path likelihood clean-up;
- Marginal likelihood estimator minor behavior changes.

28 lines of code changed in 2 files:

• src/dr/inference/mcmc: MCMC.java (+4 -4), MarginalLikelihoodEstimator.java (+24 -20)

msuchard 2010-01-06 17:15 Rev.: 2748

Added a very simple path sampling example and some minor tweaks to GMRF skyrides and the TraitGibbsOperator

74 lines of code changed in 1 file:

• src/dr/inference/mcmc: MarginalLikelihoodEstimator.java (+74 -29)

msuchard 2010-01-06 15:01 Rev.: 2747

Started working on Beta-distributed path sampling paths

112 lines of code changed in 1 file:

• src/dr/inference/mcmc: MarginalLikelihoodEstimator.java (+112 -32)

alexander.alekseyenko 2009-12-24 05:42 Rev.: 2720

making path sampling work for computing Bayes Factors; changes:
- new class that can combine MCMC operator schedules
- marginalLikelihoodEstimator can take multiple mcmc objects now
- changed format of PathSamplingAnalysis output (e.g. can copy-paste the pathParameter vs. meanPathLikelihood into a plotting program for evaluation and integration)

20 lines of code changed in 1 file:

• src/dr/inference/mcmc: MarginalLikelihoodEstimator.java (+20 -4)

rambaut 2009-10-29 05:18 Rev.: 2482

Added some simple timing round the evaluation just after each operator which is stored by the operator and reported in the operator analysis table. On this note, I have added an attribute to <mcmc operatorAnalaysis="analysis.file"> which gives the name of the file to write the analysis to. If this isn't there then the file isn't written. We need to add this to BEAUti to use the same file name stem as the log and trees file (with an extension '.ops'?).

46 lines of code changed in 2 files:

• src/dr/inference/mcmc: MCMC.java (+40 -1), MCMCParser.java (+6)

rambaut 2009-10-24 12:48 Rev.: 2460

Implemented checks to see that all models, likelihood and parameters are being controlled by the MCMC. The checks are made in MCMCParser but the warnings are currently commented out.

23 lines of code changed in 1 file:

• src/dr/inference/mcmc: MCMCParser.java (+23 -2)

rambaut 2009-10-09 00:10 Rev.: 2365

I have created an options dialog box that appears when the "-option" command line is used. I suggest we use this for the Mac OS X and Windows executables. It provides the ability to change the seed, number of threads, switch on BEAGLE and select the input file.

1 lines of code changed in 1 file:

• src/dr/inference/mcmc: MCMC.java (+1 -1)

rambaut 2009-10-06 22:37 Rev.: 2351

Now resets operators' acceptance counts after the coercion delay period.

5 lines of code changed in 1 file:

• src/dr/inference/mcmc: MCMC.java (+5)

rambaut 2009-10-06 21:19 Rev.: 2350

Updated MCMC parser rules for 'autoOptimizeDelay'.

1 lines of code changed in 1 file:

• src/dr/inference/mcmc: MCMCParser.java (+1)

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).

41 lines of code changed in 4 files:

• src/dr/inference/mcmc: MCMC.java (+20 -60), MCMCOptions.java (+6 -6), MCMCParser.java (+7 -2), MarginalLikelihoodEstimator.java (+8 -8)

jheled 2009-09-07 08:06 Rev.: 2202

Turn inlined expressions into variables for easier debugging.

2 lines of code changed in 2 files:

• src/dr/inference/mcmc: MCMCCriterion.java (new)

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