Directory src/dr/inference/model/

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msuchard 2013-04-29 03:42 Rev.: 5619

Added missing CompoundParameter.fireParameterChangedEvent method, and demonstrating a nicer approach to multi-developer debugging.

5 lines of code changed in 2 files:

• src/dr/inference/model: CompoundParameter.java (+5)

msuchard 2013-04-28 06:43 Rev.: 5617

Stream-lining serial operations during multi-parameter updates

17 lines of code changed in 2 files:

• src/dr/inference/model: Parameter.java (+17 -15)

msuchard 2013-04-19 06:30 Rev.: 5599

Debugging flag to check for thread-level parallelization of likelihood evaluations

10 lines of code changed in 2 files:

• src/dr/inference/model: CompoundLikelihood.java (+10 -1)

msuchard 2013-03-27 06:44 Rev.: 5545

Fixed memory allocation bug introduced in previous commit.

1 lines of code changed in 2 files:

• src/dr/inference/model: DiagonalMatrix.java (new)

msuchard 2013-03-27 03:48 Rev.: 5544

Implemented a log-determinant routine for numerical stability and fixed getParameterValue in DiagonalMatrix

58 lines of code changed in 1 file:

• src/dr/inference/model: DiagonalMatrix.java (+58 -25)

msuchard 2013-03-27 03:29 Rev.: 5543

Fix to issue 687; may need to port to 1.7 branch. RandomWalkOperator no longer reflects negative values when using default bounds.

10 lines of code changed in 2 files:

• src/dr/inference/model: Variable.java (new)

msuchard 2013-03-19 18:02 Rev.: 5509

Fixed log determinate for large diagonal matrices; refactored transforms.

3 lines of code changed in 2 files:

• src/dr/inference/model: MatrixParameter.java (new)

msuchard 2013-03-04 16:17 Rev.: 5466

Fixed bounds that individual parameters induce when constrained equal.

36 lines of code changed in 2 files:

• src/dr/inference/model: EqualityConstrainedParameter.java (+36 -40)

msuchard 2013-03-03 15:46 Rev.: 5465

Prototype Parameter.class to constraint equality among parameters; seems more consistent with usage than a Model.class

292 lines of code changed in 3 files:

• src/dr/inference/model: EqualityConstrainedParameter.java (+253), EqualityConstraintModel.java (new)

msuchard 2013-03-01 16:40 Rev.: 5461

Prototype Model.class to constraint equality among parameters.

142 lines of code changed in 1 file:

• src/dr/inference/model: EqualityConstraintModel.java (+142)

rambaut 2013-01-10 05:31 Rev.: 5303

Drifting

182 lines of code changed in 1 file:

• src/dr/inference/model: CompositeParameter.java (new 182)

msuchard 2013-01-10 05:20 Rev.: 5302

Added unit-IntervalLatentLiabilityLikelihood for VNTRs; plan to refactor to remove duplicated code once more fully tested.

8 lines of code changed in 1 file:

• src/dr/inference/model: CompoundParameter.java (+8 -8)

msuchard 2012-11-29 11:06 Rev.: 5261

Composition parameters; should really be a Statistic with signaling ability

127 lines of code changed in 3 files:

• src/dr/inference/model: MixtureModelLikelihood.java (new), ProductParameter.java (new 125)

alexander.alekseyenko 2012-11-20 09:35 Rev.: 5244

renamed integratedMixtureModel to MixtureModelLikelihood. Preserved an alias parser <integratedMixtureModel> per Marc's request. Updated the class, such that the mixtures are always normalized internally when likelihood is calculated.

246 lines of code changed in 2 files:

• src/dr/inference/model: IntegratedMixtureModel.java (del), MixtureModelLikelihood.java (+246 -67)

alexander.alekseyenko 2012-11-17 11:24 Rev.: 5238

Started on a model to compute mixtures of likelihoods.

107 lines of code changed in 1 file:

• src/dr/inference/model: MixtureModelLikelihood.java (+107)

msuchard 2012-11-08 10:08 Rev.: 5217

Attempting a first-order MRF prior for VNTR diffusion

104 lines of code changed in 1 file:

• src/dr/inference/model: MarkovRandomFieldMatrix.java (new 104)

msuchard 2012-11-03 14:44 Rev.: 5213

Added missing multivariate distribution likelihood model; opens up so many possibilities for rate models. Caution: may have broken Brownian diffusion precision Gibbs sampler.

29 lines of code changed in 2 files:

• src/dr/inference/model: DefaultModel.java (new)

msuchard 2012-10-28 14:36 Rev.: 5211

Implemented transposed matrix representations for multilocus branch rate models

28 lines of code changed in 3 files:

• src/dr/inference/model: MatrixParameter.java (+9 -18), TransposedMatrixParameter.java (new)

mtolkoff@gmail.com 2012-10-25 09:49 Rev.: 5206

reverts to previous version

50 lines of code changed in 1 file:

• src/dr/inference/model: MatrixParameter.java (+50 -67)

mtolkoff@gmail.com 2012-10-25 08:02 Rev.: 5205

Adds commented out broken code

114 lines of code changed in 2 files:

• src/dr/inference/model: MatrixParameter.java (+67 -49), TransposedMatrixParameter.java (+47 -3)

mtolkoff@gmail.com 2012-10-19 09:15 Rev.: 5198

Test commit; no functionality changes

11 lines of code changed in 1 file:

• src/dr/inference/model: MatrixParameter.java (+11)

msuchard 2012-10-05 09:02 Rev.: 5185

Started a wrapper to provide the transpose of a MatrixParameter

74 lines of code changed in 1 file:

• src/dr/inference/model: TransposedMatrixParameter.java (+74)

rambaut 2012-09-13 08:04 Rev.: 5155

Ported fix for issue 664 from branch 1.7.

1 lines of code changed in 1 file:

• src/dr/inference/model: CompoundLikelihood.java (+1 -1)

rambaut 2012-08-18 02:36 Rev.: 5141

Removing debug code...

14 lines of code changed in 1 file:

• src/dr/inference/model: CompoundLikelihood.java (+14 -14)

rambaut 2012-08-17 21:06 Rev.: 5137

Changed compound likelihood to return the actual special values (i.e. +Inf, NaN or -Inf) up the chain. Added 'todo' comment in MarkovChain suggesting a check for +Inf and NaN. Need to review this idea.

9 lines of code changed in 1 file:

• src/dr/inference/model: CompoundLikelihood.java (+9 -7)

rambaut 2012-08-15 22:34 Rev.: 5133

Porting changes 5131 and 5132 from 1.7 branch.

4 lines of code changed in 1 file:

• src/dr/inference/model: CompoundLikelihood.java (+4 -3)

rambaut 2012-08-08 10:19 Rev.: 5107

Porting 'evaluateLate' interface method from 1.7 branch.

89 lines of code changed in 11 files:

• src/dr/inference/model: AbstractModelLikelihood.java (new), BooleanLikelihood.java (new), CompoundLikelihood.java (+56 -32), Likelihood.java (new), PathLikelihood.java (new), ThreadedCompoundLikelihood.java (+4)

rambaut 2012-08-04 09:47 Rev.: 5100

Creating more consistent thread pool settings (-1 auto sizing thread pool, 0 thread pool off, >0 user-specified thread pool size).

4 lines of code changed in 1 file:

• src/dr/inference/model: CompoundLikelihood.java (+4 -2)

rambaut 2012-08-04 03:49 Rev.: 5097

Porting fixes from 1.7.3 back into the trunk

2 lines of code changed in 1 file:

• src/dr/inference/model: Likelihood.java (+2 -3)

jheled@gmail.com 2012-07-23 14:13 Rev.: 5077

Improve report sent by BEAST when initial posterior is infinite

12 lines of code changed in 1 file:

• src/dr/inference/model: Likelihood.java (+12 -5)

msuchard 2012-05-24 10:26 Rev.: 4998

Generifying IntegratedMixtureModel, so that one can use a mixture of DistributionLikelihood as well.

14 lines of code changed in 1 file:

• src/dr/inference/model: IntegratedMixtureModel.java (new 14)

rambaut 2012-05-18 10:59 Rev.: 4987

Imported patch attachd to issue 430 - a PearsonCorrelation statistic.

57 lines of code changed in 1 file:

• src/dr/inference/model: PearsonCorrelation.java (new 57)

rambaut 2012-05-17 23:17 Rev.: 4982

Cleaning up some of the user-info text on threading.

26 lines of code changed in 1 file:

• src/dr/inference/model: CompoundLikelihood.java (+26 -4)

rambaut 2012-05-17 20:47 Rev.: 4979

Fix for issue with multi-threading not working. The issue was that -threads 0 was being treated as no-multithreading where as it should specify an automatic thread pool size (having no -threads option gives a thread 0 value). For best performance the default should be not to use the thread command line option (but -threads 1 should be used to turn off multithreading). This also affected -beagle_instances as these use the threadpool.

9 lines of code changed in 1 file:

• src/dr/inference/model: CompoundLikelihood.java (+9 -8)

msuchard 2012-05-11 11:24 Rev.: 4950

Hopefully resolves issue 618. Codon-partitioned models do not throw XML errors with ancestral sequence reconstruction. There is still an issue with the "count" parameter name for non-dNdS robust counting. So, non-dNdS robust counting is temporarily disabled for CP models.

39 lines of code changed in 1 file:

• src/dr/inference/model: IntegratedMixtureModel.java (+39 -10)

msuchard 2012-03-15 04:26 Rev.: 4839

Reverting dimension accessors to be consistent with getParameterValue() in MatrixParameter.

28 lines of code changed in 1 file:

• src/dr/inference/model: MatrixParameter.java (+28 -3)

rambaut 2012-03-13 03:10 Rev.: 4826

Fixed issue with date parameter

11 lines of code changed in 2 files:

• src/dr/inference/model: Statistic.java (+11 -1)

rambaut 2012-03-10 02:54 Rev.: 4807

Added caching - 10 fold speed increase

3 lines of code changed in 1 file:

• src/dr/inference/model: MatrixParameter.java (+3 -3)

rambaut 2012-03-09 23:30 Rev.: 4806

Work on AG.

18 lines of code changed in 1 file:

• src/dr/inference/model: Parameter.java (+18 -1)

msuchard 2012-03-09 08:33 Rev.: 4803

Implemented a "not statistics" for boolean stats (like monophylyl). NotStatistic is now deprecated.

60 lines of code changed in 1 file:

• src/dr/inference/model: NotBooleanStatistic.java (new 60)

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