Directory src/dr/math/distributions/

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msuchard 2013-05-03 07:25 Rev.: 5628

Fixed log determine of a matrix and positive-definite check in WishartDistribution; there is still an error in LUPDecomposition.isPD()

5 lines of code changed in 2 files:

• src/dr/math/distributions: WishartDistribution.java (+5 -7)

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

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

72 lines of code changed in 6 files:

• src/dr/math/distributions: HalfTDistribution.java (new), InverseWishartDistribution.java (+29 -4), WishartDistribution.java (+2 -6), WishartStatistics.java (new 39)

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

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

53 lines of code changed in 1 file:

• src/dr/math/distributions: HalfTDistribution.java (+53)

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

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

31 lines of code changed in 1 file:

• src/dr/math/distributions: WishartDistribution.java (+31 -5)

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

Fixed log determinate for large diagonal matrices; refactored transforms.

50 lines of code changed in 2 files:

• src/dr/math/distributions: MultivariateNormalDistribution.java (new)

msuchard 2013-02-16 07:58 Rev.: 5419

Keep Colt flag off unless shown to provide more reliable simulants.

7 lines of code changed in 2 files:

• src/dr/math/distributions: GammaDistribution.java (+7 -8)

baele.guy@gmail.com 2013-02-16 00:48 Rev.: 5411

- nextGamma(alpha, lambda) in Colt needs to be called with 1/scale instead of scale
- also replaced log(x/scale) by log(x) - log(scale) to avoid numerical errors when evaluating very small values from a gamma distribution

23 lines of code changed in 1 file:

• src/dr/math/distributions: GammaDistribution.java (+23 -20)

msuchard 2013-02-07 06:29 Rev.: 5383

Side-stepping trouble with Gamma RV generation

16 lines of code changed in 1 file:

• src/dr/math/distributions: GammaDistribution.java (+16 -1)

alexander.alekseyenko 2012-10-26 09:32 Rev.: 5209

Updated Compound DirichletMultinomial distribution to use both the rates and frequencies + dispersion parametrization. New example XML included.

90 lines of code changed in 2 files:

• src/dr/math/distributions: MultivariatePolyaDistributionLikelihood.java (new)

mdhall272@gmail.com 2012-10-03 00:44 Rev.: 5184

Allowed to take infinite maximum or minimum values

21 lines of code changed in 2 files:

• src/dr/math/distributions: TruncatedNormalDistribution.java (new)

baele.guy@gmail.com 2012-10-02 08:33 Rev.: 5182

Added log transformed kernel density estimation to the list

1 lines of code changed in 2 files:

• src/dr/math/distributions: KernelDensityEstimatorDistribution.java (+1)

baele.guy@gmail.com 2012-10-02 08:31 Rev.: 5181

Kernel density estimation for densities with bounded support by using log transformation

382 lines of code changed in 1 file:

• src/dr/math/distributions: LogTransformedNormalKDEDistribution.java (new 382)

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

Porting 'evaluateLate' interface method from 1.7 branch.

4 lines of code changed in 1 file:

• src/dr/math/distributions: MultivariatePolyaDistributionLikelihood.java (+4)

dong.w.xie@gmail.com 2012-03-12 09:24 Rev.: 4816

trunk: merge prior dialog and distribution changes to trunk

29 lines of code changed in 9 files:

• src/dr/math/distributions: GammaDistribution.java (+5 -2), InverseGammaDistribution.java (+2 -3), LaplaceDistribution.java (new), LogNormalDistribution.java (+6), TruncatedDistribution.java (new)

rambaut 2012-03-08 23:56 Rev.: 4796

Fix to last commit.

1 lines of code changed in 1 file:

• src/dr/math/distributions: TruncatedDistribution.java (+1 -1)

rambaut 2012-03-08 22:09 Rev.: 4795

TruncatedDistribution now adjusts its bounds to be inside the source distribution's (i.e., if it is an OffsetPositive). LogNormalDistribution had a lower bound of -Inf, now set to zero.

9 lines of code changed in 2 files:

• src/dr/math/distributions: LogNormalDistribution.java (+1 -1), TruncatedDistribution.java (+8)

rambaut 2012-03-08 05:30 Rev.: 4788

Runtime errors galore.

19 lines of code changed in 2 files:

• src/dr/math/distributions: NormalDistribution.java (new)

rambaut 2012-03-08 04:38 Rev.: 4783

Initial, horribly slow, inefficient re-write of antigenic likelihood.

5 lines of code changed in 1 file:

• src/dr/math/distributions: NormalDistribution.java (+5)

dong.w.xie@gmail.com 2012-02-27 10:40 Rev.: 4730

trunk: merge

12 lines of code changed in 1 file:

• src/dr/math/distributions: TruncatedDistribution.java (+12 -4)

rambaut 2012-02-16 20:40 Rev.: 4701

Fix for Issue 581 - NormalDistribution was hanging when asked for a CDF when stdev was 0. Now uses better CDF function (that was already implemented) that has bound checking.

4 lines of code changed in 1 file:

• src/dr/math/distributions: NormalDistribution.java (+4 -3)

tbcbedford@gmail.com 2011-11-22 02:04 Rev.: 4468

Fixed bug in calculation of log density in BiasedMultivariateDiffusionModel. Branches should properly scale with time now. This seems to be working.

3 lines of code changed in 1 file:

• src/dr/math/distributions: MultivariateNormalDistribution.java (+3)

rambaut 2011-11-06 02:48 Rev.: 4391

Oops. Messed up implementing logPDF for UniformDistribution.

1 lines of code changed in 2 files:

• src/dr/math/distributions: UniformDistribution.java (new)

rambaut 2011-11-01 21:59 Rev.: 4384

Trying to fix up the confusion with uniform bounds. The parameter object in beauti now has 'uniformUpper' and 'uniformLower' rather than using the truncationUpper/Lower (uniform prior cannot be truncated now). Changed the logPDF function of UniformDistribution to take the log before the reciprocal to reduce chance of underflow (note however that taking the log of Double.MAX_VALUE (or twice that if the lower bound is -MAX_VALUE) may still fail). Testing now being undertaken...

6 lines of code changed in 1 file:

• src/dr/math/distributions: UniformDistribution.java (+6 -1)

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

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

11 lines of code changed in 1 file:

• src/dr/math/distributions: WishartDistribution.java (+11 -7)

msuchard 2011-09-22 10:36 Rev.: 4330

Fixed integer overflow (when prior sampling) and mixed-math in RandomWalkOperator

1 lines of code changed in 1 file:

• src/dr/math/distributions: NormalDistribution.java (+1 -1)

msuchard 2011-09-09 06:05 Rev.: 4299

Fixed prior graphs in BEAUti, inverse gamma cdf and started stochastic Dollo

4 lines of code changed in 1 file:

• src/dr/math/distributions: InverseGammaDistribution.java (+4 -1)

rambaut 2011-07-31 11:53 Rev.: 4146

Seem to have got the Antigenic MDS working correctly with threshold assay values and replicate measurements.

34 lines of code changed in 1 file:

• src/dr/math/distributions: NormalDistribution.java (+34)

rambaut 2011-07-28 11:42 Rev.: 4131

An approximation to the tail of a normal distribution added. To be tested...

73 lines of code changed in 1 file:

• src/dr/math/distributions: NormalDistribution.java (+73 -41)

rambaut 2011-07-27 23:43 Rev.: 4123

Removed commons-maths-2.0.jar from lib folder

160 lines of code changed in 1 file:

• src/dr/math/distributions: GammaDistribution.java (+160 -102)

rambaut 2011-07-26 03:18 Rev.: 4119

TruncatedDistribution more robustly handles quantiles.

41 lines of code changed in 3 files:

• src/dr/math/distributions: BetaDistribution.java (+1 -1), TruncatedDistribution.java (+40 -17)

rambaut 2011-07-16 01:40 Rev.: 4111

Generalized TruncatedDistribution that wraps another distribution. Quantile functions are not robust.

11 lines of code changed in 1 file:

• src/dr/math/distributions: TruncatedDistribution.java (+11 -2)

rambaut 2011-06-25 04:09 Rev.: 4068

Some major refactoring of PriorDialog. Probably horribly broken but at least it compiles.

126 lines of code changed in 1 file:

• src/dr/math/distributions: TruncatedDistribution.java (+126)

rambaut 2011-06-22 01:40 Rev.: 4057

Cleaned up PriorDialog to better render distributions if possible.

50 lines of code changed in 3 files:

• src/dr/math/distributions: BetaDistribution.java (+48 -14), OffsetPositiveDistribution.java (new)

msuchard 2011-05-20 03:50 Rev.: 3982

Bounds checking on Dirchlet distribution

6 lines of code changed in 2 files:

• src/dr/math/distributions: DirichletDistribution.java (new)

akaruiws 2011-04-01 18:56 Rev.: 3921

Tidy up more msatBMA related things.

1 lines of code changed in 1 file:

• src/dr/math/distributions: UniformDistribution.java (+1 -1)

denise.kuehnert@gmail.com 2011-03-25 14:31 Rev.: 3901

231 lines of code changed in 1 file:

• src/dr/math/distributions: BetaDistribution.java (+231)

dong.w.xie 2011-02-15 09:08 Rev.: 3796

Trunk: big change of new Tracer, and this check-in starts using List instead array in Variate.

20 lines of code changed in 7 files:

• src/dr/math/distributions: BetaKDEDistribution.java (+2 -2), GammaKDEDistribution.java (+2 -2), KernelDensityEstimatorDistribution.java (+10 -3), NormalKDEDistribution.java (+6 -6)

alexander.alekseyenko 2010-09-25 04:58 Rev.: 3571

Started MV Polya Likelihood model

245 lines of code changed in 1 file:

• src/dr/math/distributions: MultivariatePolyaDistributionLikelihood.java (+245)

alexei.drummond 2010-07-28 15:48 Rev.: 3335

removed unmappable character

35 lines of code changed in 1 file:

• src/dr/math/distributions: GammaKDEDistribution.java (+35 -44)

msuchard 2010-07-15 02:04 Rev.: 3314

Bifractional diffusion is a pain

3 lines of code changed in 2 files:

• src/dr/math/distributions: BifractionalDiffusionDensity.java (new)

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