February 2010 Commit Log

Number of Commits:
112
Number of Active Developers:
9
msuchard 2010-02-27 09:30 Rev.: 2990

(1) More testing of robust counting; (2) more work on a citation framework

343 lines of code changed in 7 files:

msuchard 2010-02-26 15:54 Rev.: 2989

Apologies for missing this file.

65 lines of code changed in 1 file:

msuchard 2010-02-26 15:46 Rev.: 2988

Added JUnitTest for counting synonymous jumps; also refactored a function in making codon models to avoid duplicating code

223 lines of code changed in 7 files:

dong.w.xie 2010-02-26 14:25 Rev.: 2987

Trunk refactoring: 1st part of operators (split parsers).

212 lines of code changed in 9 files:

msuchard 2010-02-26 08:31 Rev.: 2986

Sampling missing values appears to also be working

15 lines of code changed in 2 files:

msuchard 2010-02-26 08:20 Rev.: 2985

Missing data in IntegratedMultivariateTraitLikelihood appears to be working; use "NA" in taxon trait.

221 lines of code changed in 3 files:

dong.w.xie 2010-02-25 16:35 Rev.: 2984

Trunk refactoring: finish statistic model (split parsers).

964 lines of code changed in 49 files:

msuchard 2010-02-25 16:20 Rev.: 2983

Made some comments about handling missing trait values for the integrateTraitLikelihood

72 lines of code changed in 2 files:

dong.w.xie 2010-02-25 15:52 Rev.: 2982

Trunk refactoring: organize distribution parsers again.

804 lines of code changed in 19 files:

dong.w.xie 2010-02-25 15:36 Rev.: 2981

Trunk refactoring: finish distribution (split parsers).

534 lines of code changed in 23 files:

msuchard 2010-02-25 15:04 Rev.: 2980

Product chain test is now working for 2-state cross 2-state model; next will write a test for nucleotide cross nucleotide cross nucleotide

107 lines of code changed in 3 files:

dong.w.xie 2010-02-25 13:51 Rev.: 2979

Trunk refactoring: organize distribution parsers.

543 lines of code changed in 20 files:

dong.w.xie 2010-02-25 09:45 Rev.: 2978

Trunk refactoring: finish Likelihoods (split parsers)..

203 lines of code changed in 7 files:

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

Still working on product chain models and robust counting

159 lines of code changed in 4 files:

dong.w.xie 2010-02-25 09:08 Rev.: 2976

Trunk refactoring: fix bug caused by r2974.

2 lines of code changed in 2 files:

rambaut 2010-02-25 04:55 Rev.: 2975

Trying to get AbstractMultivariateTraitLikelihood to work with EmpricalTreeSampling

6 lines of code changed in 3 files:

dong.w.xie 2010-02-24 16:25 Rev.: 2974

Trunk refactoring: 1st part of Likelihoods (split parsers)..

400 lines of code changed in 27 files:

dong.w.xie 2010-02-24 15:20 Rev.: 2973

Trunk refactoring: finish rate operators (split parsers)..

212 lines of code changed in 10 files:

dong.w.xie 2010-02-24 14:50 Rev.: 2972

Trunk refactoring: finish tree operators (split parsers)..

474 lines of code changed in 25 files:

dong.w.xie 2010-02-24 11:53 Rev.: 2970

Trunk refactoring: correct ExchangeOperatorParser in operators (split parsers)..

98 lines of code changed in 6 files:

dong.w.xie 2010-02-24 11:18 Rev.: 2969

Trunk refactoring: 1st part of operators (split parsers)..

477 lines of code changed in 19 files:

msuchard 2010-02-24 03:53 Rev.: 2965

Intermediate steps in implementing robust counting of S and N using nucleotide models

809 lines of code changed in 8 files:

msuchard 2010-02-24 03:52 Rev.: 2964

Refactoring MarkovJumpsCore after Asger Hobolth reminded me that one wants to compute more than just the mean process

56 lines of code changed in 6 files:

msuchard 2010-02-24 03:39 Rev.: 2963

Allow parser options to *not* condense site patterns into a unique list; this is necessary for robust counting of S and N mutations

18 lines of code changed in 2 files:

msuchard 2010-02-24 03:36 Rev.: 2962

Fixed jitter for IntegratedMultivariateTraitLikelihood

64 lines of code changed in 6 files:

Sibon.Li@gmail.com 2010-02-23 14:55 Rev.: 2961

Fixed my last commit

16 lines of code changed in 4 files:

Sibon.Li@gmail.com 2010-02-23 14:38 Rev.: 2960

Modified MixtureModelBranchRates to not have to take in quantiles

156 lines of code changed in 2 files:

dong.w.xie 2010-02-23 09:35 Rev.: 2959

Trunk refactoring: finish tree likihood model (split parsers)..

423 lines of code changed in 22 files:

rambaut 2010-02-23 01:11 Rev.: 2958

Updated the Trunk version number to reflect that this will be heading towards v1.6.0. Updated date range to reflect 8 years of BEAST development!

3 lines of code changed in 1 file:

dong.w.xie 2010-02-22 14:29 Rev.: 2957

Trunk refactoring: finish tree model (split parsers)..

721 lines of code changed in 35 files:

dong.w.xie 2010-02-22 13:49 Rev.: 2956

Trunk refactoring: 1st part of tree model (split parsers)..

438 lines of code changed in 26 files:

dong.w.xie 2010-02-22 11:31 Rev.: 2955

Trunk: solve Issue 279: Add variance and stand error to Tracer.

23 lines of code changed in 2 files:

dong.w.xie 2010-02-22 10:42 Rev.: 2954

Trunk refactoring: organize tree and treelikelihood parsers.

834 lines of code changed in 35 files:

dong.w.xie 2010-02-22 10:07 Rev.: 2953

Trunk refactoring: finish speciation (split parsers)..

561 lines of code changed in 30 files:

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

192 lines of code changed in 2 files:

msuchard 2010-02-20 08:07 Rev.: 2951

Testing different scalings in multivariate trait model

26 lines of code changed in 5 files:

msuchard 2010-02-20 06:15 Rev.: 2950

Continuing work on a unified citation mechanism

186 lines of code changed in 5 files:

rambaut 2010-02-20 02:02 Rev.: 2949

Local clocks on the stem lineages only.

25 lines of code changed in 2 files:

philippe.lemey@gmail.com 2010-02-20 00:56 Rev.: 2948

RateIndicatorBF tweaking

3 lines of code changed in 1 file:

msuchard 2010-02-19 15:56 Rev.: 2947

Fixed small bug in pre-order traversal in IntegratedTraitLikelihood

41 lines of code changed in 2 files:

dong.w.xie 2010-02-19 15:20 Rev.: 2946

Trunk refactoring: 1st part of speciation (split parsers)..

147 lines of code changed in 8 files:

dong.w.xie 2010-02-19 15:12 Rev.: 2945

Trunk refactoring: move dr.evomodel.operators.TreeNodeSlide to TREE OPERATORS category.

1 lines of code changed in 1 file:

dong.w.xie 2010-02-19 14:54 Rev.: 2944

Trunk refactoring: finish Random Local Yule Model (split parsers).

456 lines of code changed in 21 files:

dong.w.xie 2010-02-19 14:41 Rev.: 2943

Trunk refactoring: finish coalescent (split parsers).

1362 lines of code changed in 48 files:

dong.w.xie 2010-02-19 10:08 Rev.: 2942

Trunk refactoring: 2nd part of coalescent (split parsers).

304 lines of code changed in 18 files:

dong.w.xie 2010-02-18 16:36 Rev.: 2941

Trunk refactoring: finish branch rate and clock rate model (split parsers).

291 lines of code changed in 12 files:

dong.w.xie 2010-02-18 16:25 Rev.: 2940

Trunk refactoring: 1st part of coalescent (split parsers).

1220 lines of code changed in 42 files:

dong.w.xie 2010-02-18 10:12 Rev.: 2939

Trunk refactoring: branch rate and clock rate model (split parsers).

915 lines of code changed in 32 files:

philippe.lemey@gmail.com 2010-02-18 00:24 Rev.: 2938

RateIndicatorBF tweaking

12 lines of code changed in 1 file:

philippe.lemey@gmail.com 2010-02-17 22:59 Rev.: 2937

TimeSlicer tweaking and bug fixing

13 lines of code changed in 1 file:

dong.w.xie 2010-02-17 16:12 Rev.: 2936

Trunk refactoring: make evoxml parsers more organized.

483 lines of code changed in 57 files:

dong.w.xie 2010-02-17 16:04 Rev.: 2935

Trunk refactoring: make subst parsers more organized.

1922 lines of code changed in 69 files:

dong.w.xie 2010-02-17 15:45 Rev.: 2934

Trunk refactoring: site model (split parsers).

421 lines of code changed in 22 files:

dong.w.xie 2010-02-17 15:15 Rev.: 2933

Trunk: fix bugs, parser should return the exact model type referred.

5 lines of code changed in 3 files:

dong.w.xie 2010-02-17 15:09 Rev.: 2932

Trunk: fix BinaryCovarionModelParser bug.

1 lines of code changed in 1 file:

dong.w.xie 2010-02-17 14:56 Rev.: 2931

Trunk refactoring: complex substitution model (split parsers).

342 lines of code changed in 11 files:

dong.w.xie 2010-02-17 12:29 Rev.: 2930

Trunk refactoring: finish substitution model (split parsers).

383 lines of code changed in 13 files:

dong.w.xie 2010-02-17 12:00 Rev.: 2929

Trunk refactoring: big part of substitution model (split parsers).

467 lines of code changed in 19 files:

dong.w.xie 2010-02-17 10:32 Rev.: 2928

Trunk refactoring: fix BEAUti generator.

18 lines of code changed in 2 files:

dong.w.xie 2010-02-17 10:25 Rev.: 2927

Trunk refactoring: substitution model - binary (spilt parsers).

361 lines of code changed in 14 files:

msuchard 2010-02-16 20:52 Rev.: 2926

(1) Small fix to trait rate Gibbs operator and (2) initial classes for robust counting on codon partitioned models

168 lines of code changed in 3 files:

msuchard 2010-02-16 16:28 Rev.: 2925

Added a Gibbs sampler for branch-rate parameters under a scaled mixture of normals diffusion model

191 lines of code changed in 5 files:

dong.w.xie 2010-02-16 15:30 Rev.: 2924

Trunk refactoring: RandomTaxaSampleParser.

121 lines of code changed in 3 files:

dong.w.xie 2010-02-16 13:42 Rev.: 2923

Trunk: make all parsers loaded properly, from now, BeastParser only allow to keep very basic xml parsers.

133 lines of code changed in 6 files:

dong.w.xie 2010-02-16 12:05 Rev.: 2922

Trunk: The intermediate exchange operator is deprecated for unknown reason, therefore comment out its parser to make other 2 parsers registered properly.

5 lines of code changed in 3 files:

dong.w.xie 2010-02-16 11:54 Rev.: 2921

Trunk: start to move all parsers from BeastParser.java into release_parsers.properties.

252 lines of code changed in 2 files:

dong.w.xie 2010-02-16 11:17 Rev.: 2920

Trunk: more correction.

1 lines of code changed in 2 files:

dong.w.xie 2010-02-16 10:55 Rev.: 2919

Trunk: fix build.

189 lines of code changed in 2 files:

dong.w.xie 2010-02-16 10:52 Rev.: 2918

Trunk: correct spelling.

1 lines of code changed in 1 file:

alexei.drummond 2010-02-15 16:25 Rev.: 2917

random walks improvement

9 lines of code changed in 1 file:

alexei.drummond 2010-02-15 16:12 Rev.: 2916

implemented inhomogeneous random walk from KML-based lattice

355 lines of code changed in 4 files:

dong.w.xie 2010-02-15 16:07 Rev.: 2915

Trunk: update more SnAphl GUI.

105 lines of code changed in 2 files:

alexei.drummond 2010-02-15 14:56 Rev.: 2914

Use image for rendering, started consolidating viewtransform code in single class

191 lines of code changed in 5 files:

dong.w.xie 2010-02-15 14:42 Rev.: 2913

Trunk: update SnAphl GUI.

133 lines of code changed in 2 files:

alexei.drummond 2010-02-15 14:15 Rev.: 2912

LinkedList was horrifically slow in Polygon2D for polygons of >100000 vertices. Added a general KMLViewer...

521 lines of code changed in 9 files:

dong.w.xie 2010-02-11 14:24 Rev.: 2911

Trunk: record result for further diagnose.

89 lines of code changed in 1 file:

dong.w.xie 2010-02-11 09:16 Rev.: 2910

Trunk: add new test without enable, because it has problem.

231 lines of code changed in 1 file:

dong.w.xie 2010-02-10 16:16 Rev.: 2909

Trunk: update test.

29 lines of code changed in 1 file:

dong.w.xie 2010-02-10 16:04 Rev.: 2908

Trunk: update tesst.

295 lines of code changed in 5 files:

rambaut 2010-02-10 03:57

Resolved an arbitrary contraction of a constant name.

630 lines of code changed in 4 files:

dong.w.xie 2010-02-09 14:55 Rev.: 2905

Trunk: add more test.

335 lines of code changed in 1 file:

dong.w.xie 2010-02-09 14:01 Rev.: 2904

Trunk: disable another test class with problem.

122 lines of code changed in 2 files:

dong.w.xie 2010-02-09 12:55 Rev.: 2903

Trunk: enable more test of Operator and disable 2 test classes with problem.

303 lines of code changed in 5 files:

dong.w.xie 2010-02-09 10:22 Rev.: 2902

Trunk: continue to fight to constant String.

6 lines of code changed in 2 files:

dong.w.xie 2010-02-09 10:14 Rev.: 2901

Trunk: fight to constant String.

7 lines of code changed in 2 files:

dong.w.xie 2010-02-09 09:55 Rev.: 2899

Trunk: delete duplicate xml.

0 lines of code changed in 2 files:

alexei.drummond 2010-02-09 07:02 Rev.: 2898

Further work on geographic diffusion with boundaries

149 lines of code changed in 12 files:

dong.w.xie 2010-02-08 17:07 Rev.: 2897

Trunk: fix previous bug.

1 lines of code changed in 1 file:

dong.w.xie 2010-02-08 16:44 Rev.: 2896

Trunk: add new test for clock rate.

258 lines of code changed in 4 files:

alexei.drummond 2010-02-05 17:47 Rev.: 2895

Class to look at joint geographical diffusion probs

126 lines of code changed in 2 files:

alexei.drummond 2010-02-05 16:59 Rev.: 2894

Better color function for visualizing geographical transition probabilities

67 lines of code changed in 2 files:

alexei.drummond 2010-02-05 15:42 Rev.: 2889

Computing numerical transition probabilities for 2D diffusion with arbitrary well boundaries

594 lines of code changed in 13 files:

dong.w.xie 2010-02-05 15:15 Rev.: 2887

Trunk: enable general sub model test, and correct the rate1 expectation in xml.

361 lines of code changed in 4 files:

dong.w.xie 2010-02-05 13:49 Rev.: 2886

Trunk: test for random local clock, but the model has problem, so that the test is not actived for Hudson.

268 lines of code changed in 1 file:

dong.w.xie 2010-02-05 11:31 Rev.: 2885

Trunk: update SnAPhyl GUI.

742 lines of code changed in 13 files:

alexei.drummond 2010-02-05 09:06 Rev.: 2884

Further work on SpaceTime simulation

499 lines of code changed in 10 files:

msuchard 2010-02-04 17:49 Rev.: 2883

Fixed determinant computation bug in MultivariateNormalDistribution

2 lines of code changed in 1 file:

dong.w.xie 2010-02-04 13:46 Rev.: 2882

Trunk: update test.

44 lines of code changed in 4 files:

alexei.drummond 2010-02-04 13:45 Rev.: 2881

Example reconstructs a phylogeographic path given a three taxa tree with specied end-point locations

58 lines of code changed in 2 files:

alexei.drummond 2010-02-04 11:24 Rev.: 2880

Added some cities and fixed the superclass

30 lines of code changed in 3 files:

jen.tom 2010-02-04 09:26 Rev.: 2879

a kernel density estimator with Gamma kernel

118 lines of code changed in 1 file:

dong.w.xie 2010-02-04 09:15 Rev.: 2878

Trunk: update test.

5 lines of code changed in 2 files:

dong.w.xie 2010-02-03 10:11 Rev.: 2876

Trunk: hide the confused constructor from MCMC.

31 lines of code changed in 8 files:

dong.w.xie 2010-02-03 10:04 Rev.: 2875

Trunk: add new test for log normal prior.

126 lines of code changed in 1 file:

dong.w.xie 2010-02-03 09:57 Rev.: 2874

Trunk: incomplete correction of 2state coarion model, and leave to Alexei to complete.

24 lines of code changed in 2 files:

alexei.drummond 2010-02-03 09:09 Rev.: 2873

Added parser for Tanja's birth-death serial sampling model

99 lines of code changed in 2 files:

dong.w.xie 2010-02-02 15:32 Rev.: 2872

Trunk: merge r2871 from branch.

1 lines of code changed in 1 file:

alexei.drummond 2010-02-02 14:57 Rev.: 2870

Alexei and Marc realizing that rejection sampling in 2D map of Europe is difficult: absorptive versus reflective coastlines should give different answers.

373 lines of code changed in 6 files:

dong.w.xie 2010-02-02 14:55 Rev.: 2869

Trunk: Fix error in r2866 to maintaining JDK 1.5 compatibility, by replacing push to addFirst.

3 lines of code changed in 2 files:

jheled 2010-02-02 14:29 Rev.: 2868

Do a 2 or 1 node move if that is all node can do. add test files for tree uniform operators.

345 lines of code changed in 4 files:

msuchard 2010-02-02 13:59 Rev.: 2867

Removing non-UTF characters.

1 lines of code changed in 2 files:

alexander.alekseyenko 2010-02-02 11:31 Rev.: 2866

Started on Population Tree Approximation models.

459 lines of code changed in 9 files:

January 2010 »

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