December 2009 Commit Log

Number of Commits:
55
Number of Active Developers:
6
msuchard 2009-12-30 11:47 Rev.: 2723

Now can add jitter to equal (or all) trait values.

99 lines of code changed in 1 file:

msuchard 2009-12-30 05:22 Rev.: 2722

Trait randomization now can take an array of bounds

16 lines of code changed in 1 file:

msuchard 2009-12-24 06:17 Rev.: 2721

Fixed regular polygon parser

114 lines of code changed in 2 files:

alexander.alekseyenko 2009-12-24 05:42 Rev.: 2720

making path sampling work for computing Bayes Factors; changes:
- new class that can combine MCMC operator schedules
- marginalLikelihoodEstimator can take multiple mcmc objects now
- changed format of PathSamplingAnalysis output (e.g. can copy-paste the pathParameter vs. meanPathLikelihood into a plotting program for evaluation and integration)

133 lines of code changed in 3 files:

philippe.lemey@gmail.com 2009-12-24 04:15 Rev.: 2719

DiscreteRatePriorGenerator tweaks

68 lines of code changed in 1 file:

Sibon.Li@gmail.com 2009-12-23 17:11 Rev.: 2718

Added MixtureModelBranchRates

4 lines of code changed in 2 files:

Sibon.Li@gmail.com 2009-12-23 17:10 Rev.: 2717

Added work in progress to discretizedBranchRates to allow for normalising of the mean branch rate (does not yet work properly but does not effect existing operations)

85 lines of code changed in 2 files:

Sibon.Li@gmail.com 2009-12-23 11:17 Rev.: 2716

Removed normalised mean rate function of TreeLogger

20 lines of code changed in 2 files:

msuchard 2009-12-23 05:06 Rev.: 2715

Finished some code to randomize initial trait values

21 lines of code changed in 1 file:

msuchard 2009-12-22 12:15 Rev.: 2714

Working on arbitrary branch rates for a real scaled mixture of normals

27 lines of code changed in 2 files:

dong.w.xie 2009-12-22 11:35 Rev.: 2713

Trunk: merge r2712

18 lines of code changed in 5 files:

Sibon.Li@gmail.com 2009-12-22 10:53 Rev.: 2711

Tidied up some code

13 lines of code changed in 3 files:

Sibon.Li@gmail.com 2009-12-22 10:41 Rev.: 2710

Created tool MixtureModelLogAnalyser which can parses discrete variables in the log trace

346 lines of code changed in 1 file:

msuchard 2009-12-22 05:20 Rev.: 2709

Working on arbitrary branch rates for a real scaled mixture of normals

53 lines of code changed in 1 file:

rambaut 2009-12-19 04:29 Rev.: 2708

Some very minor fixes

18 lines of code changed in 4 files:

dong.w.xie 2009-12-18 10:02 Rev.: 2707

Trunk: merge r2706

33 lines of code changed in 1 file:

msuchard 2009-12-18 06:09 Rev.: 2705

Finished refactoring spatial distributions and implemented an approximate diffusion on a sphere using the von Mises-Fisher distribution

430 lines of code changed in 12 files:

rambaut 2009-12-18 03:53 Rev.: 2704

Some work on an improved version of CoalGen.

411 lines of code changed in 9 files:

dong.w.xie 2009-12-17 13:00 Rev.: 2703

Trunk: merge r2702

1 lines of code changed in 1 file:

dong.w.xie 2009-12-16 15:55 Rev.: 2701

Trunk: merge r2700

66 lines of code changed in 4 files:

dong.w.xie 2009-12-16 10:01 Rev.: 2699

Trunk: merge Issue 268

6 lines of code changed in 2 files:

msuchard 2009-12-15 07:46 Rev.: 2698

Ant build should now work.

0 lines of code changed in 1 file:

msuchard 2009-12-15 06:40 Rev.: 2697

Refactoring geo-specific functionality into dr.geo (step 1). Also, adding in shell classes for many different spatial distributions

590 lines of code changed in 23 files:

msuchard 2009-12-14 11:45 Rev.: 2696

Going to use the von Mises-Fisher distribution to approximate symmetric diffusion on a sphere

104 lines of code changed in 2 files:

rambaut 2009-12-12 03:50 Rev.: 2694

Have implemented a NodeHeightsStatistic. This produces an ordered list of node heights. If given a groupSize statistic then it will group them accordingly. This allows us to write a demographic log file that contains the population sizes and change points for Skyline and Skyride plots:
<log id="demoLog" logEvery="5000" fileName="gmrf.demo">
<parameter idref="skyride.logPopSize"/>
<nodeHeightsStatistic id="changePoint">
<treeModel idref="treeModel"/>
</nodeHeightsStatistic>
</log>

<log id="demoLog" logEvery="5000" fileName="bsp.demo">
<parameter idref="skyline.popSize"/>
<parameter idref="skyline.groupSize"/>
<nodeHeightsStatistic id="changePoint">
<treeModel idref="treeModel"/>
<parameter idref="skyline.groupSize"/>
</nodeHeightsStatistic>
</log>

3 lines of code changed in 1 file:

rambaut 2009-12-12 02:14 Rev.: 2693

Added parser for new NodeHeightStatistic.

2 lines of code changed in 2 files:

rambaut 2009-12-12 02:12 Rev.: 2692

Failed to update a few files after last commit..

171 lines of code changed in 6 files:

rambaut 2009-12-12 01:47 Rev.: 2691

Minor correction of intercapitalization.

175 lines of code changed in 7 files:

msuchard 2009-12-11 04:25 Rev.: 2690

Started SDE modeling for diffusion

36 lines of code changed in 1 file:

dong.w.xie 2009-12-10 16:25 Rev.: 2689

Trunk: merge from branch 1.5 in

5 lines of code changed in 1 file:

dong.w.xie 2009-12-10 16:15 Rev.: 2688

Trunk: merge from branch 1.5 in

1 lines of code changed in 1 file:

dong.w.xie 2009-12-10 16:03

Trunk: merge from branch 1.5 in

44 lines of code changed in 3 files:

dong.w.xie 2009-12-10 15:57 Rev.: 2683

Trunk: start merge parser from branch 1.5 in

43 lines of code changed in 3 files:

dong.w.xie 2009-12-10 15:49 Rev.: 2682

Trunk: merge BEAUti from branch 1.5 in

15 lines of code changed in 3 files:

dong.w.xie 2009-12-10 15:29 Rev.: 2681

Trunk: start merge BEAST main from branch 1.5 in

65 lines of code changed in 7 files:

dong.w.xie 2009-12-10 15:16 Rev.: 2680

Trunk: start merge parser from branch 1.5 in

7 lines of code changed in 1 file:

dong.w.xie 2009-12-10 13:55 Rev.: 2679

Trunk: start merge parser from branch 1.5 in

52 lines of code changed in 2 files:

dong.w.xie 2009-12-10 13:44 Rev.: 2678

Trunk: start merge BEAUti from branch 1.5 in

1407 lines of code changed in 45 files:

dong.w.xie 2009-12-10 13:34 Rev.: 2675

Trunk: start merge from branch 1.5 in

15901 lines of code changed in 69 files:

msuchard 2009-12-10 05:36 Rev.: 2673

MarkovJumps now supports Markov reward processes. Also a typo fix in BeastMain and some unnecessary casting in AMTL.

257 lines of code changed in 10 files:

rambaut 2009-12-05 05:33 Rev.: 2656

Fix for dynamic scaling with BEAGLE?

17 lines of code changed in 1 file:

Sibon.Li@gmail.com 2009-12-04 16:58 Rev.: 2655

Uploaded two new relaxed clock implementations/models, RandomDiscretizedBranchRates and MixtureModelBranchRates.

691 lines of code changed in 4 files:

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:

msuchard 2009-12-03 07:14 Rev.: 2651

Started work on bifractional continuous random walk models

111 lines of code changed in 2 files:

Sibon.Li@gmail.com 2009-12-02 16:57 Rev.: 2650

Modified text output from NormaliseMeanTreeRate

2 lines of code changed in 2 files:

Sibon.Li@gmail.com 2009-12-02 16:56 Rev.: 2649

Fixed bug with TreeParameterModel where double should've been used instead of int

4 lines of code changed in 1 file:

Sibon.Li@gmail.com 2009-12-02 16:49 Rev.: 2648

LogNormalDistribution isMeanInRealSpace is actually defaulted to false

1 lines of code changed in 1 file:

dong.w.xie 2009-12-02 13:16 Rev.: 2646

Trunk: move all arg from release into development in both branch and trunk, which means it would be unavailable in the release version but available in development. That is determined by parsers=development or parsers=release in beast.properties

29 lines of code changed in 2 files:

dong.w.xie 2009-12-02 12:59 Rev.: 2643

Trunk: merge parser.

3 lines of code changed in 2 files:

rambaut 2009-12-02 00:07 Rev.: 2642

Trying to get JVM 1.5 linking compatibility

5 lines of code changed in 4 files:

dong.w.xie 2009-12-01 14:07 Rev.: 2641

Trunk: remove thread = null.

1 lines of code changed in 1 file:

rambaut 2009-12-01 10:37 Rev.: 2639

Recompilation of beagle.jar to try and fix a JVM mismatch

0 lines of code changed in 1 file:

rambaut 2009-12-01 09:57 Rev.: 2638

Fixed a compilation issue for Java 1.5.

2 lines of code changed in 1 file:

rambaut 2009-12-01 08:55 Rev.: 2637

Fixed a compilation issue for Java 1.5.

55 lines of code changed in 3 files:

rambaut 2009-12-01 03:37 Rev.: 2636

Added drag and drop of log files into Tracer.

1220 lines of code changed in 19 files:

November 2009 »

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