January 2010 Commit Log

Number of Commits:
62
Number of Active Developers:
9
msuchard 2010-01-29 16:26 Rev.: 2861

Simple stupid solution to the Italian problem.

28 lines of code changed in 3 files:

dong.w.xie 2010-01-29 16:09 Rev.: 2860

Trunk: Maintaining JDK 1.5 compatibility.

4 lines of code changed in 2 files:

alexei.drummond 2010-01-29 15:41 Rev.: 2859

Alexei and Marc adding 2-dimensional brownian bridge with rejection-sampling on map of Europe :-)

278 lines of code changed in 4 files:

dong.w.xie 2010-01-29 14:38 Rev.: 2858

Trunk: update test.

168 lines of code changed in 3 files:

dong.w.xie 2010-01-29 11:12 Rev.: 2857

Trunk: update Junit test for tree likelihood.

192 lines of code changed in 1 file:

msuchard 2010-01-29 11:08 Rev.: 2856

Refactoring multivariate normal distribution to support nice Brownian bridge features

107 lines of code changed in 2 files:

alexei.drummond 2010-01-29 09:53 Rev.: 2855

Alexei and Marc adding N-dimensional brownian bridge with rejection-sampling!

197 lines of code changed in 5 files:

dong.w.xie 2010-01-29 09:52 Rev.: 2854

Trunk: add and enable new Junit test for tree likelihood.

185 lines of code changed in 3 files:

alexander.alekseyenko 2010-01-29 07:44 Rev.: 2853

Fixed burn-in issues in MLE, restructured integration procedure, now using Integrator classes for handling different integration schemes.

146 lines of code changed in 2 files:

dong.w.xie 2010-01-28 14:34 Rev.: 2852

Trunk: update LikelihoodTest integration test.

44 lines of code changed in 1 file:

msuchard 2010-01-28 13:46 Rev.: 2851

Started tests for and debugging of bifractional diffusion density. Look: a JUnit

307 lines of code changed in 2 files:

dong.w.xie 2010-01-28 13:45 Rev.: 2850

Trunk: make a new integration test.

226 lines of code changed in 2 files:

msuchard 2010-01-27 21:19 Rev.: 2849

More work on bifractional diffusion. Finally have some reasonable densities.

451 lines of code changed in 4 files:

dong.w.xie 2010-01-27 14:56 Rev.: 2847

Trunk: some corrections of integration test.

78 lines of code changed in 3 files:

alexei.drummond 2010-01-27 12:34 Rev.: 2846

Marc and Alexei added joint likelihood calculation and test for ancestral state likelihood

133 lines of code changed in 3 files:

dong.w.xie 2010-01-27 10:41 Rev.: 2844

Trunk: add integration test MCMCTest, and enable it in Hudson.

53 lines of code changed in 4 files:

dong.w.xie 2010-01-27 09:53 Rev.: 2843

Trunk: correct test.

17 lines of code changed in 1 file:

msuchard 2010-01-26 18:16 Rev.: 2840

Bug fixes for integrated Brownian diffusion.

225 lines of code changed in 3 files:

dong.w.xie 2010-01-26 16:08 Rev.: 2839

Trunk: more test.

228 lines of code changed in 3 files:

dong.w.xie 2010-01-26 10:18 Rev.: 2838

Trunk: finish testMCMC test, but need verification.

34 lines of code changed in 1 file:

msuchard 2010-01-25 20:11 Rev.: 2837

Integrated Brownian diffusion now supports full conditional sampling of internal nodes.

367 lines of code changed in 4 files:

sidneym 2010-01-25 17:22 Rev.: 2836

Update copyright dates and in so doing test commit messages

1 lines of code changed in 2 files:

dong.w.xie 2010-01-25 15:07 Rev.: 2835

Trunk: update testMCMC test.

38 lines of code changed in 1 file:

msuchard 2010-01-25 13:43 Rev.: 2834

Working on integrating out Brownian diffusion internal node traits

236 lines of code changed in 4 files:

jheled 2010-01-25 10:32 Rev.: 2833

don't fail on incomplete tree logs

12 lines of code changed in 1 file:

alexei.drummond 2010-01-22 11:29 Rev.: 2830

Marc and Alexei added discrete trait based branch rate model - yay

1585 lines of code changed in 7 files:

msuchard 2010-01-22 07:01 Rev.: 2829

Improved numerical stability for von Mises-Fisher distribution

5 lines of code changed in 4 files:

rambaut 2010-01-22 04:53 Rev.: 2828

Updates to Java BEAGLE. BEAST now compiles and runs but make not be correct yet when using BEAGLE.

169 lines of code changed in 5 files:

dong.w.xie 2010-01-21 13:11 Rev.: 2827

Trunk: fix seed for integration test, and see whether to solve unstable Hudson test.

13 lines of code changed in 3 files:

msuchard 2010-01-21 12:33 Rev.: 2826

Implementing Dirk Brockmann's suggestions on computing fractional diffusion densities

52 lines of code changed in 2 files:

dong.w.xie 2010-01-21 10:38 Rev.: 2825

Trunk: merge r2824 from branch.

5 lines of code changed in 2 files:

dong.w.xie 2010-01-21 10:27 Rev.: 2823

Trunk: update SnAPhylApp.

25 lines of code changed in 4 files:

dong.w.xie 2010-01-20 18:09 Rev.: 2822

Trunk: add images and rename to SnAPhylApp.

131 lines of code changed in 6 files:

dong.w.xie 2010-01-20 17:47

Trunk: try to fix code breaking caused by IntelliJ.

2589 lines of code changed in 9 files:

dong.w.xie 2010-01-20 17:40 Rev.: 2819

Trunk: try to fix code breaking caused by IntelliJ.

2057 lines of code changed in 16 files:

dong.w.xie 2010-01-20 17:18 Rev.: 2818

Trunk: initial code for project SnAPhyl GUI (using part of BEAUti code).

1566 lines of code changed in 12 files:

msuchard 2010-01-19 07:13 Rev.: 2816

Was computing conditional precision for trait imputation wrong

7 lines of code changed in 1 file:

dong.w.xie 2010-01-18 16:10 Rev.: 2815

Trunk: add new test draft.

170 lines of code changed in 2 files:

msuchard 2010-01-18 14:07 Rev.: 2814

Fixed bug in TimeSlicer; was using wrong precision matrix

18 lines of code changed in 2 files:

philippe.lemey@gmail.com 2010-01-18 00:20 Rev.: 2813

TimeSlicer tweaking and bug fixing

23 lines of code changed in 1 file:

alexander.alekseyenko 2010-01-17 10:15 Rev.: 2811

Minor changes to Path Sampling Marginal Likelihood Estimation and Bayes Factor analysis, including:
- Operator analysis printer class (general purpose);
- Operator schedule, critical bug fix;
- Path likelihood clean-up;
- Marginal likelihood estimator minor behavior changes.

202 lines of code changed in 6 files:

philippe.lemey@gmail.com 2010-01-17 04:16 Rev.: 2810

TimeSlicer tweaking and bug fixing

61 lines of code changed in 1 file:

msuchard 2010-01-16 09:11 Rev.: 2809

Very simple slice sampler appears to work

117 lines of code changed in 6 files:

msuchard 2010-01-16 07:40

Starting to implement a generic univariate slice sampler

438 lines of code changed in 9 files:

akaruiws 2010-01-13 15:04 Rev.: 2799

One JUnit test name corrected.

1 lines of code changed in 1 file:

akaruiws 2010-01-13 14:54 Rev.: 2798

More examples added.

97 lines of code changed in 2 files:

akaruiws 2010-01-13 13:54 Rev.: 2797

Add more JUnit tests.

4 lines of code changed in 1 file:

akaruiws 2010-01-13 13:28 Rev.: 2796

JUnit test for full likelihood calculation with microsatellite model.

76 lines of code changed in 1 file:

philippe.lemey@gmail.com 2010-01-12 07:40 Rev.: 2795

TimeSlicer tweaking: added in branch sets

179 lines of code changed in 1 file:

philippe.lemey@gmail.com 2010-01-12 01:11 Rev.: 2794

TimeSlicer bug fixing and reinstating TAB-delimited output

502 lines of code changed in 1 file:

philippe.lemey@gmail.com 2010-01-11 22:49 Rev.: 2793

TimeSlicer bug fixing and reinstating TAB-delimited output

37 lines of code changed in 1 file:

msuchard 2010-01-11 13:16 Rev.: 2792

GMRF Skyride appears to be missing a normalization constant; will try to fix in next commit.

207 lines of code changed in 3 files:

msuchard 2010-01-11 08:46 Rev.: 2791

Fix for von Mises-Fisher diffusion model and add pseudo-densities to PathLikelihood calculations

51 lines of code changed in 2 files:

akaruiws 2010-01-09 15:13 Rev.: 2790

Allow multiple independent random walks for different indices of the same parameter.

110 lines of code changed in 1 file:

akaruiws 2010-01-09 15:02 Rev.: 2789

The scope of some variables have been changed to allow extension.

4 lines of code changed in 1 file:

msuchard 2010-01-09 05:42 Rev.: 2788

Added a very simple path sampling example involving a phylogenetic problem (2-taxon tree, testing \kappa = 10 vs \kappa random)

91 lines of code changed in 2 files:

msuchard 2010-01-06 17:15 Rev.: 2748

Added a very simple path sampling example and some minor tweaks to GMRF skyrides and the TraitGibbsOperator

369 lines of code changed in 5 files:

msuchard 2010-01-06 15:01 Rev.: 2747

Started working on Beta-distributed path sampling paths

114 lines of code changed in 2 files:

dong.w.xie 2010-01-05 09:07 Rev.: 2727

Trunk: Re-adding xml file deleted in r2675

224 lines of code changed in 1 file:

msuchard 2010-01-01 03:49 Rev.: 2726

Updated TraitGibbsOperator so that it defaults to only sampling tips that have priors.

27 lines of code changed in 1 file:

msuchard 2010-01-01 03:47 Rev.: 2725

Re-adding version of file that shows how to use Markov rewards

11 lines of code changed in 1 file:

msuchard 2010-01-01 03:30 Rev.: 2724

Re-adding two files deleted in r2673 (why?)

164 lines of code changed in 2 files:

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