StatSVN - Directory src/dr/math/

Author	Changes	Lines of Code	Lines per Change
Totals	150 (100.0%)	8786 (100.0%)	58.5
msuchard	58 (38.7%)	4772 (54.3%)	82.2
gerton.lunter	9 (6.0%)	2058 (23.4%)	228.6
alexei.drummond	35 (23.3%)	924 (10.5%)	26.4
rambaut	17 (11.3%)	757 (8.6%)	44.5
Michael.DefoinPLatel	2 (1.3%)	113 (1.3%)	56.5
jheled	17 (11.3%)	86 (1.0%)	5.0
dong.w.xie	1 (0.7%)	21 (0.2%)	21.0
Sibon.Li@gmail.com	1 (0.7%)	20 (0.2%)	20.0
bloomquist	3 (2.0%)	16 (0.2%)	5.3
alexander.alekseyenko	3 (2.0%)	14 (0.2%)	4.6
akaruiws	4 (2.7%)	5 (0.1%)	1.2

Most Recent Commits

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.

0 lines of code changed in 2 files:

src/dr/math: MathUtils.java (-15)

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

Started on a model to compute mixtures of likelihoods.

14 lines of code changed in 1 file:

src/dr/math: MathUtils.java (+14)

msuchard 2012-01-10 02:55 Rev.: 4572

Adding a CnCs counting class

0 lines of code changed in 2 files:

src/dr/math: EmpiricalBayesPoissonSmoother.java (new)

msuchard 2012-01-05 06:26 Rev.: 4570

Modified EB Poisson smoother for sampling distribution

52 lines of code changed in 1 file:

src/dr/math: EmpiricalBayesPoissonSmoother.java (+52 -3)

msuchard 2011-07-30 03:51 Rev.: 4144

Fixed shrinkage issue when variance is too low

5 lines of code changed in 1 file:

src/dr/math: EmpiricalBayesPoissonSmoother.java (+5)

msuchard 2011-06-19 05:46 Rev.: 4043

Fixed bug in Procrustes and added UnitTest.

14 lines of code changed in 2 files:

src/dr/math: Procrustes.java (new)

rambaut 2011-06-19 01:17 Rev.: 4042

Further tweaks to Procrustes

42 lines of code changed in 1 file:

src/dr/math: Procrustes.java (+42 -31)

rambaut 2011-06-19 00:38 Rev.: 4041

Can now apply the configured procrustes transformation to other vectors (say, coordinates at internal nodes of the tree).

41 lines of code changed in 1 file:

src/dr/math: Procrustes.java (+41 -7)

rambaut 2011-06-18 23:55 Rev.: 4040

Procrustination is working I think.

17 lines of code changed in 1 file:

src/dr/math: Procrustes.java (+17 -21)

rambaut 2011-06-18 22:43 Rev.: 4039

Added the as yet untested procrustination into AntigenicPlotter.

1 lines of code changed in 1 file:

src/dr/math: Procrustes.java (+1 -1)

rambaut 2011-06-18 09:56 Rev.: 4037

Work on porting procrustes.r

62 lines of code changed in 1 file:

src/dr/math: Procrustes.java (+62 -21)

msuchard 2011-06-18 01:56 Rev.: 4035

Added translational hints about R code

13 lines of code changed in 1 file:

src/dr/math: Procrustes.java (+13)

rambaut 2011-06-17 23:42 Rev.: 4034

Start of a port of the R procrustination function

60 lines of code changed in 1 file:

src/dr/math: Procrustes.java (+60)

msuchard 2011-04-10 03:59 Rev.: 3931

Work on dependent evolution between pairs of amino acids

13 lines of code changed in 1 file:

src/dr/math: EmpiricalBayesPoissonSmoother.java (+13 -1)

msuchard 2011-04-09 08:55 Rev.: 3928

Fixed numerical instability in empirical Bayes smoother for a Poisson-Gamma model

21 lines of code changed in 1 file:

src/dr/math: EmpiricalBayesPoissonSmoother.java (+21 -1)

akaruiws 2010-09-08 10:06 Rev.: 3505

Added methods for computing the transition probabilities.

4 lines of code changed in 2 files:

src/dr/math: ModifiedBesselFirstKind.java (new)

alexei.drummond 2010-09-07 23:08 Rev.: 3502

49 lines of code changed in 1 file:

src/dr/math: ModifiedBesselFirstKind.java (+49)

msuchard 2010-07-14 20:56 Rev.: 3312

Mighty cool positive selection tools through simple nucleotide models.

37 lines of code changed in 1 file:

src/dr/math: EmpiricalBayesPoissonSmoother.java (+37)

msuchard 2010-06-30 00:27 Rev.: 3296

Tool for performing KDE using a Gaussian kernel (most standard approach)

210 lines of code changed in 2 files:

src/dr/math: ComplexArray.java (new 59), FastFourierTransform.java (new 151)

akaruiws 2010-06-06 22:12 Rev.: 3233

Misc changes to classes for msat likelihood calculation.

1 lines of code changed in 2 files:

src/dr/math: MersenneTwisterFast.java (new)

msuchard 2010-03-03 12:49 Rev.: 3014

Delegating funcationality in IntegratedMultivariateTraitLikelihood for profiling and future refactoring into a TraitLikelihoodCore

37 lines of code changed in 2 files:

src/dr/math: KroneckerOperation.java (+37)

msuchard 2010-02-25 09:43 Rev.: 2977

Still working on product chain models and robust counting

46 lines of code changed in 1 file:

src/dr/math: KroneckerOperation.java (+46 -4)

msuchard 2010-02-21 08:06 Rev.: 2952

Added Kronecker product and sum operations; will be used for product chain substitution models for robust counting

92 lines of code changed in 1 file:

src/dr/math: KroneckerOperation.java (+92)

msuchard 2009-12-04 06:42 Rev.: 2653

Can now compute the Mittag-Leffler function for real arguments; necessary for modeling bifractional diffusion

303 lines of code changed in 1 file:

src/dr/math: MittagLefflerFunction.java (new 303)

Sibon.Li@gmail.com 2009-09-24 17:02 Rev.: 2293

Changed input format of ACLikelihood to allow incorporating other distributions (logSpace="true"/"false" replaced with distribution="logNormal"/"normal"/"inverseGaussian"

20 lines of code changed in 1 file:

src/dr/math: MathUtils.java (+20 -1)

dong.w.xie 2009-08-24 18:25 Rev.: 2129

BEAUTi:
1) cotinue Issue #100;
2) start Issue #124.

21 lines of code changed in 1 file:

src/dr/math: MathUtils.java (+21)

msuchard 2009-07-26 09:33 Rev.: 1918

Implemented a Monte Carlo integral estimator in UniformNodeHeightPrior.

8 lines of code changed in 2 files:

src/dr/math: LogTricks.java (new)

msuchard 2009-07-25 12:13 Rev.: 1917

Bullet-proofing (or attempting to do so) eigen-decomposition and singular value decomposition. The Robust* classes are bug-hunting and temporary.

17 lines of code changed in 1 file:

src/dr/math: MathUtils.java (+17)

rambaut 2009-07-18 04:01 Rev.: 1869

A few minor bits for project with John and Marc

48 lines of code changed in 2 files:

src/dr/math: Polynomial.java (new)

rambaut 2009-05-26 02:21 Rev.: 1743

Seem to have a working UniformRootPrior.

20 lines of code changed in 1 file:

src/dr/math: Polynomial.java (+20 -20)

msuchard 2009-05-13 11:41 Rev.: 1707

2 lines of code changed in 1 file:

src/dr/math: Polynomial.java (+2 -2)

msuchard 2009-05-13 11:38 Rev.: 1706

Commented out arbitrary precision polynomials; am still not happy with them.

141 lines of code changed in 1 file:

src/dr/math: Polynomial.java (+141 -141)

msuchard 2009-05-13 11:25 Rev.: 1705

Working on Welch's uniform prior; should now work for < 30 taxa

661 lines of code changed in 2 files:

src/dr/math: LogTricks.java (+6 -4), Polynomial.java (+655)

jheled 2009-05-01 09:55 Rev.: 1660

don't go belly up when passed negative values. masking some situation which should be handled better - in this case the UPGMA trees having zero length branches leading to a bug in the coalecent code.

5 lines of code changed in 2 files:

src/dr/math: Binomial.java (new)

jheled 2009-04-09 13:26 Rev.: 1546

Add convenience uniform method

16 lines of code changed in 1 file:

src/dr/math: MathUtils.java (+16 -8)

bloomquist 2009-03-12 10:18 Rev.: 1491

Rate variation appears to be working. In fact, it seems to be working very well! For now, old arg stuff will not work, but will fix as soon as possible.

3 lines of code changed in 1 file:

src/dr/math: MathUtils.java (+3)

msuchard 2008-12-25 08:54 Rev.: 1397

Tweaked BeastParser so that it only reports parser loadings under verbose-mode. Added dr.geo package to hold non-evolutionary geospatial stuff.

16 lines of code changed in 1 file:

src/dr/math: IntegrableUnivariateFunction.java (new 16)

jheled 2008-11-19 12:11 Rev.: 1318

Code Police

2 lines of code changed in 2 files:

src/dr/math: ConjugateDirectionSearch.java (+2 -2)

bloomquist 2008-09-09 11:53 Rev.: 1180

These are some files I have been working on for about 2 weeks. The only changes outisde of the GMRF stuff is a logHyperSphereVolume in MathUtils. It provides the log(volume) for a sphere in n dimensions with radius r.

6 lines of code changed in 1 file:

src/dr/math: MathUtils.java (+6)

msuchard 2008-08-14 11:09 Rev.: 1126

Port of ARG classes into the trunk. There are some very silly repeats of code (namely: TreeModel and ARGModel should inherit from a base class, ARGTreeLogger is almost indentical to TreeLogger, and CompoundParameter should replace ARGCompoundParameter).

68 lines of code changed in 2 files:

src/dr/math: MathUtils.java (+32), MersenneTwisterFast.java (+36 -4)

(52 more)

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