Directory src/dr/inferencexml/model/

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msuchard 2013-03-20 12:29 Rev.: 5512

Fixed transform; they were missing Jacobians in computing densities.

3 lines of code changed in 2 files:

• src/dr/inferencexml/model: CompoundLikelihoodParser.java (+3 -2)

mdhall272@gmail.com 2013-02-18 22:32 Rev.: 5424

ProductStatistics now take the ID of the relevant XML object as a name if they do not otherwise have one (so the relevant columns in the log file and hence in Tracer will not simply be called "productStatistic"). This is how SumStatistic already works.

9 lines of code changed in 2 files:

• src/dr/inferencexml/model: ProductStatisticParser.java (new)

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

Composition parameters; should really be a Statistic with signaling ability

79 lines of code changed in 1 file:

• src/dr/inferencexml/model: ProductParameterParser.java (new 79)

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

Attempting a first-order MRF prior for VNTR diffusion

82 lines of code changed in 1 file:

• src/dr/inferencexml/model: MarkovRandomFieldMatrixParser.java (new 82)

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/inferencexml/model: CompoundLikelihoodParser.java (+4 -4)

msuchard 2012-08-12 12:03 Rev.: 5124

Fixing thread pools: -1 = auto, 0 = single, >0 = pool

1 lines of code changed in 1 file:

• src/dr/inferencexml/model: CompoundLikelihoodParser.java (+1 -1)

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).

6 lines of code changed in 1 file:

• src/dr/inferencexml/model: CompoundLikelihoodParser.java (+6 -6)

rambaut 2012-08-04 09:30 Rev.: 5098

Fixing default thread pool size back to 0 (which denotes an autosizing thread pool).

5 lines of code changed in 1 file:

• src/dr/inferencexml/model: CompoundLikelihoodParser.java (+5 -5)

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

Porting fixes from 1.7.3 back into the trunk

3 lines of code changed in 1 file:

• src/dr/inferencexml/model: CompoundLikelihoodParser.java (+3 -8)

msuchard 2012-07-10 15:52 Rev.: 5062

Fixed more -1s in thread-pools and add limited dialogue support for SSE (which sidesteps known bug in SSE phylogeography)

28 lines of code changed in 1 file:

• src/dr/inferencexml/model: CompoundLikelihoodParser.java (+28 -3)

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

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

21 lines of code changed in 1 file:

• src/dr/inferencexml/model: CompoundLikelihoodParser.java (+21 -15)

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

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

68 lines of code changed in 1 file:

• src/dr/inferencexml/model: NotBooleanStatisticParser.java (new 68)

rambaut 2011-10-11 03:46 Rev.: 4348

A slight modification to the thread pooling. Rather than just threading the 'likelihood' compoundLikelihood, it now threads the 'posterior'. To do this it flattens out all the compoundLikelihoods (i.e., 'likelihood' and 'prior'). Should allow the prior calculations to help pad some of the unused thread and load balance a bit better. Tested and works but would like to do some benchmarking.

9 lines of code changed in 1 file:

• src/dr/inferencexml/model: CompoundLikelihoodParser.java (+9 -3)

rambaut 2011-08-28 04:15 Rev.: 4245

Dirichlet stuff

14 lines of code changed in 2 files:

• src/dr/inferencexml/model: DummyLikelihoodParser.java (new)

rambaut 2011-08-24 04:16 Rev.: 4236

Added a prior on distances based on Coulombs law of charged particles repelling

64 lines of code changed in 1 file:

• src/dr/inferencexml/model: CoulombPriorParser.java (new 64)

msuchard 2011-07-21 03:39 Rev.: 4114

Removed warning, as reported on beast-users

1 lines of code changed in 2 files:

• src/dr/inferencexml/model: SumStatisticParser.java (new)

jheled 2011-03-24 13:20 Rev.: 3898

validation for RPN expressions

5 lines of code changed in 2 files:

• src/dr/inferencexml/model: RPNcalculatorStatisticParser.java (new)

msuchard 2011-03-02 14:27 Rev.: 3845

ID assigned in ReciprocalStatisticParser necessary to test normal-gamma model Gibbs samplers

1 lines of code changed in 2 files:

• src/dr/inferencexml/model: ReciprocalStatisticParser.java (+1 -1)

msuchard 2011-02-23 16:07 Rev.: 3820

Updated MaskParameter to specify mod x masking for specification of hierarchical priors in multidimensional scaling

29 lines of code changed in 2 files:

• src/dr/inferencexml/model: MaskedParameterParser.java (+29 -2)

dong.w.xie 2010-09-03 14:36 Rev.: 3486

Trunk: solve Issue 384: Unhandled attribute (typo?) name in sumStatistic:rateChanges

3 lines of code changed in 1 file:

• src/dr/inferencexml/model: SumStatisticParser.java (+3 -1)

akaruiws 2010-08-09 11:49 Rev.: 3375

Jeffrey's prior for parameters of Normal distribution.

67 lines of code changed in 1 file:

• src/dr/inferencexml/model: OneOnX3PriorParser.java (new 67)

jheled 2010-06-02 07:04 Rev.: 3211

code police

2 lines of code changed in 1 file:

• src/dr/inferencexml/model: DummyLikelihoodParser.java (+2 -3)

dong.w.xie 2010-03-25 16:56 Rev.: 3072

TRUNK: BEAUti Phylogeographic generator for general discrete traits.

3 lines of code changed in 1 file:

• src/dr/inferencexml/model: SumStatisticParser.java (+3 -2)

dong.w.xie 2010-03-03 10:42 Rev.: 3013

Trunk refactoring: finish MULTIVARIATE OU PROCESS (split parsers).

157 lines of code changed in 3 files:

• src/dr/inferencexml/model: CompoundSymmetricMatrixParser.java (new 57), DefaultModelParser.java (new 53), DiagonalMatrixParser.java (new 47)

dong.w.xie 2010-03-02 13:21 Rev.: 3003

Trunk refactoring: finish trace (split parsers).

66 lines of code changed in 1 file:

• src/dr/inferencexml/model: ThreadedCompoundLikelihoodParser.java (new 66)

dong.w.xie 2010-02-25 16:35 Rev.: 2984

Trunk refactoring: finish statistic model (split parsers).

916 lines of code changed in 15 files:

• src/dr/inferencexml/model: DifferenceStatisticParser.java (new 61), ExponentialStatisticParser.java (new 55), ExpressionStatisticParser.java (new 69), LogarithmStatisticParser.java (new 65), MeanStatisticParser.java (new 47), NegativeStatisticParser.java (new 48), NotStatisticParser.java (new 55), ProductStatisticParser.java (+66), RPNcalculatorStatisticParser.java (+73), RatioStatisticParser.java (new 48), ReciprocalStatisticParser.java (+55), SubStatisticParser.java (new 63), SumStatisticParser.java (+66), TestStatisticParser.java (new 98), VarianceStatisticParser.java (new 47)

dong.w.xie 2010-02-25 15:52 Rev.: 2982

Trunk refactoring: organize distribution parsers again.

193 lines of code changed in 3 files:

• src/dr/inferencexml/model: DuplicatedParameterParser.java (new 49), LikelihoodBenchmarkerParser.java (new 89), MaskedParameterParser.java (+55)

dong.w.xie 2010-02-25 09:08 Rev.: 2976

Trunk refactoring: fix bug caused by r2974.

2 lines of code changed in 2 files:

• src/dr/inferencexml/model: OneOnXPriorParser.java (+2 -2)

dong.w.xie 2010-02-24 16:25 Rev.: 2974

Trunk refactoring: 1st part of Likelihoods (split parsers)..

299 lines of code changed in 5 files:

• src/dr/inferencexml/model: BooleanLikelihoodParser.java (new 51), CompoundLikelihoodParser.java (+91), CompoundParameterParser.java (new 49), DummyLikelihoodParser.java (+43), OneOnXPriorParser.java (+65)