Directory src/dr/inferencexml/distribution/

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msuchard 2013-04-25 06:38 Rev.: 5610

Implemented a scaled mixture of Wishart distribution for precision matrix inference.

95 lines of code changed in 1 file:

• src/dr/inferencexml/distribution: WishartGammaDistributionModelParser.java (new 95)

msuchard 2013-04-23 14:39 Rev.: 5602

Added a half-T-distribution for more flexible specification of precision matrices in trait evolution.

136 lines of code changed in 2 files:

• src/dr/inferencexml/distribution: PriorParsers.java (+136 -92)

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

Fixed transform; they were missing Jacobians in computing densities.

2 lines of code changed in 2 files:

• src/dr/inferencexml/distribution: MultivariateNormalDistributionModelParser.java (+2 -50)

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

Fixed log determinate for large diagonal matrices; refactored transforms.

25 lines of code changed in 1 file:

• src/dr/inferencexml/distribution: MultivariateNormalDistributionModelParser.java (+25 -2)

msuchard 2013-03-12 08:53 Rev.: 5476

Improved error checking for binomial likelihood parser.

6 lines of code changed in 2 files:

• src/dr/inferencexml/distribution: BinomialLikelihoodParser.java (+6 -1)

msuchard 2013-01-23 09:47 Rev.: 5335

Added hard bounds for ancient DNA studies involving EmpiricalDistributionLikelihood

17 lines of code changed in 2 files:

• src/dr/inferencexml/distribution: EmpiricalDistributionLikelihoodParser.java (+17 -6)

msuchard 2012-11-20 08:36 Rev.: 5243

Binomial likelihood now takes non-fixed counts.

24 lines of code changed in 1 file:

• src/dr/inferencexml/distribution: BinomialLikelihoodParser.java (+24 -8)

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.

109 lines of code changed in 1 file:

• src/dr/inferencexml/distribution: MultivariateNormalDistributionModelParser.java (+109)

mdhall272@gmail.com 2012-10-12 05:31 Rev.: 5194

Committed work to date on network reconstruction method

141 lines of code changed in 1 file:

• src/dr/inferencexml/distribution: TruncatedNormalDistributionModelParser.java (new 141)

msuchard 2012-09-12 10:00 Rev.: 5152

Added skew-normal distribution model

65 lines of code changed in 1 file:

• src/dr/inferencexml/distribution: SkewNormalDistributionModelParser.java (new 65)

msuchard 2012-05-15 01:50 Rev.: 4956

Added a beta distribution model

62 lines of code changed in 1 file:

• src/dr/inferencexml/distribution: BetaDistributionModelParser.java (new 62)

gcybis@yahoo.com.br 2012-03-16 18:15 Rev.: 4863

Hierarchical model for discrete trait

79 lines of code changed in 1 file:

• src/dr/inferencexml/distribution: HierarchicalGraphLikelihoodParser.java (new 79)

baele.guy@gmail.com 2012-03-05 01:52 Rev.: 4765

Added additional prior parsers (for future use with generalized stepping-stone sampling).

194 lines of code changed in 1 file:

• src/dr/inferencexml/distribution: PriorParsers.java (+194)

dong.w.xie 2011-11-01 13:15 Rev.: 4380

trunk: solve Issue 527: change bound of Uniform prior into Double MAX or MIN, and Issue 528: the BEAST parser for UniformPrior should throw a parser exception if you attempt to give a bound at infinity.

5 lines of code changed in 1 file:

• src/dr/inferencexml/distribution: PriorParsers.java (+5)

rambaut 2011-08-20 08:37 Rev.: 4220

Fix for DPL parser. (also added 'scale' attribute to exponential as alternative to 'mean').

17 lines of code changed in 3 files:

• src/dr/inferencexml/distribution: DirichletProcessLikelihoodParser.java (new), PriorParsers.java (+14 -5)

rambaut 2011-08-20 07:04 Rev.: 4218

Parser for the Dirichlet process likelihood

79 lines of code changed in 1 file:

• src/dr/inferencexml/distribution: DirichletProcessLikelihoodParser.java (+79)

sibon.li 2011-06-21 12:46 Rev.: 4053

Transferring my changes from branch 1.6 to trunk:

Changes to LogNormalDistributionModel to allow for the stdev value to also not
be in log space (r3774)
Changes to UncorrelatedRelaxedClockTest due to changes in
LogNormalDistributionModel in r3774 (r3775)
Minor change in MixtureModelBranchRates to fix an issue caused by changes in
revision 3735 (r3773)
Bug fix for AncestralSequenceAnnotator plus added a window to select
input/output files (r3819)
Fixed spelling for GeneralSubstitutionModelTest (r3833)
Fixed a RuntimeException for AncestralStateTreeLikelihood (r3957)

9 lines of code changed in 2 files:

• src/dr/inferencexml/distribution: LogNormalDistributionModelParser.java (new)

dong.w.xie 2011-03-25 16:23 Rev.: 3902

Trunk: finish Brith Death Serial Sampling in BEAUti, but some of xmls are not running.

49 lines of code changed in 1 file:

• src/dr/inferencexml/distribution: PriorParsers.java (+49)

rambaut 2010-11-04 09:39 Rev.: 3694

Updated trunk's Laplace Prior Parser to use 'scale' rather than 'stdev' (to match the output of BEAUti and the parser in the 1.6 branch).

3 lines of code changed in 1 file:

• src/dr/inferencexml/distribution: PriorParsers.java (+3 -3)

jheled 2010-09-24 13:14 Rev.: 3570

Catch errors which lead to beast infinite loop or failure in parsers. more detailed error messages.

7 lines of code changed in 2 files:

• src/dr/inferencexml/distribution: MixedDistributionLikelihoodParser.java (new)

msuchard 2010-09-09 04:22 Rev.: 3508

Better checking in generalized linear models to ensure that design matrices are of full rank.

26 lines of code changed in 2 files:

• src/dr/inferencexml/distribution: GeneralizedLinearModelParser.java (new)

akaruiws 2010-06-11 12:47 Rev.: 3248

Msat model averaging.

138 lines of code changed in 2 files:

• src/dr/inferencexml/distribution: ModelSpecificPseudoPriorLikelihoodParser.java (new 70), TwoPartsDistributionLikelihoodParser.java (new 68)

dong.w.xie 2010-03-23 16:56 Rev.: 3067

TRUNK: BEAUti Phylogeographic initial dev done for gui.

3 lines of code changed in 2 files:

• src/dr/inferencexml/distribution: CachedDistributionLikelihoodParser.java (+3 -3)

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

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

249 lines of code changed in 2 files:

• src/dr/inferencexml/distribution: GeneralizedLinearModelParser.java (+190), RandomWalkModelParser.java (new 59)

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

Trunk refactoring: organize distribution parsers again.

593 lines of code changed in 3 files:

• src/dr/inferencexml/distribution: BinomialLikelihoodParser.java (+85), CachedDistributionLikelihoodParser.java (+59), PriorParsers.java (+449)

dong.w.xie 2010-02-25 15:36 Rev.: 2981

Trunk refactoring: finish distribution (split parsers).

454 lines of code changed in 5 files:

• src/dr/inferencexml/distribution: InverseGaussianDistributionModelParser.java (new 106), LogNormalDistributionModelParser.java (+109), MixedDistributionLikelihoodParser.java (+67), NormalDistributionModelParser.java (new 98), UniformDistributionModelParser.java (new 74)

dong.w.xie 2010-02-25 13:51 Rev.: 2979

Trunk refactoring: organize distribution parsers.

525 lines of code changed in 7 files:

• src/dr/inferencexml/distribution: DistributionLikelihoodParser.java (new 105), DistributionModelParser.java (new 92), EmpiricalDistributionLikelihoodParser.java (+132), ExponentialDistributionModelParser.java (new 34), ExponentialMarkovModelParser.java (new 94), GammaDistributionModelParser.java (new 34), OnePGammaDistributionModelParser.java (new 34)