Directory src/dr/inference/distribution/

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

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

197 lines of code changed in 3 files:

• src/dr/inference/distribution: MultivariateDistributionLikelihood.java (new), WishartGammalDistributionModel.java (new 183)

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

Fixed transform; they were missing Jacobians in computing densities.

82 lines of code changed in 3 files:

• src/dr/inference/distribution: MultivariateDistributionLikelihood.java (+80 -5), MultivariateNormalDistributionModel.java (+2 -27)

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

Fixed log determinate for large diagonal matrices; refactored transforms.

23 lines of code changed in 1 file:

• src/dr/inference/distribution: MultivariateNormalDistributionModel.java (+23 -3)

msuchard 2013-02-08 05:11 Rev.: 5384

Implemented bounds and negative offsets for empirical distributions; improved normalization.

9 lines of code changed in 2 files:

• src/dr/inference/distribution: EmpiricalDistributionLikelihood.java (+9 -4)

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

Added hard bounds for ancient DNA studies involving EmpiricalDistributionLikelihood

18 lines of code changed in 1 file:

• src/dr/inference/distribution: EmpiricalDistributionLikelihood.java (+18 -7)

mdhall272@gmail.com 2012-11-20 22:24 Rev.: 5246

Implemented user-specified starting transmission trees

1 lines of code changed in 2 files:

• src/dr/inference/distribution: TruncatedNormalDistributionModel.java (+1 -1)

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

Binomial likelihood now takes non-fixed counts.

12 lines of code changed in 2 files:

• src/dr/inference/distribution: BinomialLikelihood.java (new)

mdhall272@gmail.com 2012-11-20 02:44 Rev.: 5240

Fixed a problem with normal incubation periods

14 lines of code changed in 1 file:

• src/dr/inference/distribution: TruncatedNormalDistributionModel.java (+14 -5)

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.

253 lines of code changed in 3 files:

• src/dr/inference/distribution: MultivariateDistributionLikelihood.java (+81 -6), MultivariateNormalDistributionModel.java (+134), ParametricMultivariateDistributionModel.java (new 38)

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

Implemented transposed matrix representations for multilocus branch rate models

8 lines of code changed in 1 file:

• src/dr/inference/distribution: MultivariateDistributionLikelihood.java (+8 -8)

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

Committed work to date on network reconstruction method

209 lines of code changed in 1 file:

• src/dr/inference/distribution: TruncatedNormalDistributionModel.java (+209)

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

Added skew-normal distribution model

152 lines of code changed in 1 file:

• src/dr/inference/distribution: SkewNormalDistributionModel.java (new 152)

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

Porting 'evaluateLate' interface method from 1.7 branch.

17 lines of code changed in 2 files:

• src/dr/inference/distribution: DistributionLikelihood.java (new)

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

Improve report sent by BEAST when initial posterior is infinite

21 lines of code changed in 1 file:

• src/dr/inference/distribution: DistributionLikelihood.java (+21)

gcybis@yahoo.com.br 2012-07-09 20:35 Rev.: 5061

Better mixing for hierarchical graph model

4 lines of code changed in 2 files:

• src/dr/inference/distribution: HierarchicalGraphLikelihood.java (new)

msuchard 2012-05-15 22:19 Rev.: 4963

Fixed store/restore functionality of BetaDistributionModel

5 lines of code changed in 2 files:

• src/dr/inference/distribution: BetaDistributionModel.java (new)

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

Added a beta distribution model

180 lines of code changed in 1 file:

• src/dr/inference/distribution: BetaDistributionModel.java (+180)

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

Hierarchical model for discrete trait

162 lines of code changed in 1 file:

• src/dr/inference/distribution: HierarchicalGraphLikelihood.java (+162)

rambaut 2012-02-27 23:37 Rev.: 4734

Parser rules missing an expected element

2 lines of code changed in 1 file:

• src/dr/inference/distribution: MultivariateDistributionLikelihood.java (+2)

msuchard 2011-09-26 10:31 Rev.: 4333

Can specify non-integer degrees-of-freedom for Wishart distributions

2 lines of code changed in 1 file:

• src/dr/inference/distribution: MultivariateDistributionLikelihood.java (+2 -2)

msuchard 2011-08-25 11:52 Rev.: 4242

Tidying up DP operations.

11 lines of code changed in 2 files:

• src/dr/inference/distribution: DirichletProcessLikelihood.java (new)

rambaut 2011-08-24 23:18 Rev.: 4239

An operator that draws item allocations to clusters under the Dirichlet process.

12 lines of code changed in 1 file:

• src/dr/inference/distribution: DirichletProcessLikelihood.java (+12)

rambaut 2011-08-24 01:13 Rev.: 4232

Test suit for the DirichletProcessLikelihood

6 lines of code changed in 1 file:

• src/dr/inference/distribution: DirichletProcessLikelihood.java (+6 -5)

rambaut 2011-08-20 10:29 Rev.: 4221

Fixed up a few things.

14 lines of code changed in 1 file:

• src/dr/inference/distribution: DirichletProcessLikelihood.java (+14 -8)

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

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

5 lines of code changed in 1 file:

• src/dr/inference/distribution: DirichletProcessLikelihood.java (+5 -9)

rambaut 2011-08-20 07:11 Rev.: 4219

Couldn't resist implementing the log factorials as a look-up table.

17 lines of code changed in 1 file:

• src/dr/inference/distribution: DirichletProcessLikelihood.java (+17 -5)

rambaut 2011-08-20 06:34 Rev.: 4217

Spelling mistake and a fix to the formula.

129 lines of code changed in 2 files:

• src/dr/inference/distribution: DirechletProcessLikelihood.java (del), DirichletProcessLikelihood.java (+129)

rambaut 2011-08-20 03:57 Rev.: 4215

First stab at a Dirichlet process likelihood (no parser yet).

0 lines of code changed in 1 file:

• src/dr/inference/distribution: DirechletProcessLikelihood.java (new)

rambaut 2011-08-10 23:50 Rev.: 4179

Some refactoring of MatrixParameter (renamed getNumberOfParameters to getParameterCount). Also allowed MultivariateNormalPrior take a matrix parameter and assume the individual parameters within this represent independent draws from the MVN.

29 lines of code changed in 3 files:

• src/dr/inference/distribution: MultivariateDistributionLikelihood.java (+28 -9), RandomWalkModel.java (new)

rambaut 2011-07-24 06:42 Rev.: 4118

Reverted most of the functions of GammaDistributionModel to use the GD in dr.math. Only the quantile function uses the Commons Math version (to minimize disturbance).

3 lines of code changed in 2 files:

• src/dr/inference/distribution: GammaDistributionModel.java (new)

rambaut 2011-07-24 06:30 Rev.: 4117

Switched GammaDistributionModel to use Common Math version to see if that has better numerical stability. Also updated commons-math to the latest version.

14 lines of code changed in 1 file:

• src/dr/inference/distribution: GammaDistributionModel.java (+14 -4)

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)

22 lines of code changed in 2 files:

• src/dr/inference/distribution: LogNormalDistributionModel.java (+22 -6)

msuchard 2011-05-07 05:03 Rev.: 3969

Changed default debugging option for running empirical distribution models

1 lines of code changed in 1 file:

• src/dr/inference/distribution: EmpiricalDistributionLikelihood.java (+1 -1)

msuchard 2011-03-03 05:44 Rev.: 3847

Add functionality to read plink SNP frequencies and run continuous diffusion models

0 lines of code changed in 1 file:

• src/dr/inference/distribution: MultivariateDistributionLikelihood.java (-1)

msuchard 2011-01-04 08:37 Rev.: 3769

Slightly improved error reporting for multivariate normal parsing

3 lines of code changed in 1 file:

• src/dr/inference/distribution: MultivariateDistributionLikelihood.java (+3 -1)

alexei.drummond 2010-09-27 11:44 Rev.: 3575

Changed species tree annotations to use two double arrays: dmt and dmv to represent the times and values of the demographic function for the associated branch. This fits in with standard TreeTrait.DA() class and will be automatically annotated by TreeAnnotator and visualizable in FigTree. Some changes in *BEAST specific post-processing will be necessary but I don't have access to that code which I believe is in Python somewhere.

7 lines of code changed in 1 file:

• src/dr/inference/distribution: MultivariateDistributionLikelihood.java (+7 -4)

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

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

2 lines of code changed in 2 files:

• src/dr/inference/distribution: MixedDistributionLikelihood.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.

31 lines of code changed in 2 files:

• src/dr/inference/distribution: GeneralizedLinearModel.java (new)

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

Msat model averaging.

108 lines of code changed in 3 files:

• src/dr/inference/distribution: DistributionLikelihood.java (+1 -1), ModelSpecificPseudoPriorLikelihood.java (new 53), TwoPartsDistributionLikelihood.java (new 54)

rambaut 2010-06-08 04:20 Rev.: 3237

A few tweaks

5 lines of code changed in 1 file:

• src/dr/inference/distribution: MultivariateDistributionLikelihood.java (+5)

(103 more)