May 2012 Commit Log

Number of Commits:
55
Number of Active Developers:
7
baele.guy@gmail.com 2012-05-31 20:51 Rev.: 5003

Fixed indexing issue in the stepping-stone sampling estimator.

6 lines of code changed in 1 file:

baele.guy@gmail.com 2012-05-25 00:56 Rev.: 5002

Bugfix for the linear integrator scheme.

3 lines of code changed in 1 file:

fbielejec 2012-05-25 00:42 Rev.: 5001

edited TODO

0 lines of code changed in 1 file:

fbielejec 2012-05-25 00:41 Rev.: 5000

working on bss UI

368 lines of code changed in 5 files:

baele.guy@gmail.com 2012-05-24 22:31 Rev.: 4999

Minor change to text output.

5 lines of code changed in 1 file:

msuchard 2012-05-24 10:26 Rev.: 4998

Generifying IntegratedMixtureModel, so that one can use a mixture of DistributionLikelihood as well.

14 lines of code changed in 1 file:

fbielejec 2012-05-23 22:18 Rev.: 4997

working on parser for epoch ancestral state reco

3 lines of code changed in 1 file:

fbielejec 2012-05-23 22:13 Rev.: 4996

working on epoch ancestral state reco

27 lines of code changed in 2 files:

fbielejec 2012-05-23 21:51 Rev.: 4995

working on epoch ancestral state reco

38 lines of code changed in 1 file:

fbielejec 2012-05-22 02:05

general parser

13 lines of code changed in 2 files:

fbielejec 2012-05-21 23:45 Rev.: 4990

simplify the parser

39 lines of code changed in 3 files:

rambaut 2012-05-18 10:59 Rev.: 4987

Imported patch attachd to issue 430 - a PearsonCorrelation statistic.

113 lines of code changed in 2 files:

rambaut 2012-05-18 10:37 Rev.: 4985

Cleaned up the tipdate sampling options (the joint prior model wasn't generating code so hid this option). Removed requirement for taxon sets to be at least 2 taxa.

43 lines of code changed in 4 files:

msuchard 2012-05-18 00:39 Rev.: 4984

On second thought, it might just be easier to group several TreeParameterModels together. Committing just to keep a record.

118 lines of code changed in 6 files:

rambaut 2012-05-17 23:17 Rev.: 4982

Cleaning up some of the user-info text on threading.

47 lines of code changed in 2 files:

msuchard 2012-05-17 21:02 Rev.: 4981

Generifying TreeParameterModel to handle multiple data-types (double, double[], int, etc.). Also base abstract class supports an includeTips flag developed in TrialTreeParameterModel (now depricated). NewTreeParameterModel should replace TreeParameterModel after extensive testing.

434 lines of code changed in 3 files:

rambaut 2012-05-17 20:47 Rev.: 4979

Fix for issue with multi-threading not working. The issue was that -threads 0 was being treated as no-multithreading where as it should specify an automatic thread pool size (having no -threads option gives a thread 0 value). For best performance the default should be not to use the thread command line option (but -threads 1 should be used to turn off multithreading). This also affected -beagle_instances as these use the threadpool.

17 lines of code changed in 5 files:

rambaut 2012-05-17 01:47 Rev.: 4977

Fix for http://code.google.com/p/beast-mcmc/issues/detail?id=620 - allows taxon sets of 1 taxon if 'includeStem' is selected.

13 lines of code changed in 1 file:

rambaut 2012-05-17 01:00 Rev.: 4975

Fix for http://code.google.com/p/beast-mcmc/issues/detail?id=623. Logging multiple clock rates to tree logger now gives partition name prefixed tags.

49 lines of code changed in 1 file:

rambaut 2012-05-16 22:40 Rev.: 4973

Fix for http://code.google.com/p/beast-mcmc/issues/detail?id=627 - change in the clock group name now is propagated to the clock table popup.

1 lines of code changed in 2 files:

msuchard 2012-05-16 22:39 Rev.: 4972

Tweaks to hierarchical transmission model

4 lines of code changed in 2 files:

msuchard 2012-05-16 20:46 Rev.: 4971

Added a trait logger for complete histories with times under robust dnds counting

89 lines of code changed in 2 files:

msuchard 2012-05-16 20:26 Rev.: 4970

TreeTransforms are now loggable as branch traits

66 lines of code changed in 3 files:

rambaut 2012-05-16 11:29 Rev.: 4967

AncestralTreeLikelihood does not need a substitution model - it gets it from the site model.

0 lines of code changed in 1 file:

rambaut 2012-05-16 11:28 Rev.: 4966

Fix for issue 611: http://code.google.com/p/beast-mcmc/issues/detail?id=611
Discrete trait rates file now has a proper prefix and is not a hidden file.

2 lines of code changed in 1 file:

rambaut 2012-05-15 22:24 Rev.: 4964

Fix for issue 625: http://code.google.com/p/beast-mcmc/issues/detail?id=625
TreeLikelihood for a non codon-partitioned partition was not being given the correct prefix if there was another codon-partitioned partition.

2 lines of code changed in 1 file:

msuchard 2012-05-15 22:19 Rev.: 4963

Fixed store/restore functionality of BetaDistributionModel

31 lines of code changed in 3 files:

rambaut 2012-05-15 20:53 Rev.: 4962

Very important bug fix - the check boxes in the States panel now line up.

9 lines of code changed in 1 file:

msuchard 2012-05-15 20:51 Rev.: 4961

Starting work on a complete history filter

258 lines of code changed in 5 files:

msuchard 2012-05-15 20:50 Rev.: 4960

Expanding robust counting dNdS to consider complete histories

108 lines of code changed in 3 files:

msuchard 2012-05-15 20:24 Rev.: 4959

Fixed error last revision introduced into TreeParameterModel

1 lines of code changed in 1 file:

fbielejec 2012-05-15 11:11 Rev.: 4958

Diplomacy is about surviving until the next century. Politics is about surviving until the next Friday

48 lines of code changed in 1 file:

msuchard 2012-05-15 03:07 Rev.: 4957

Implementing a hierarchical version of the transmission model

252 lines of code changed in 6 files:

msuchard 2012-05-15 01:50 Rev.: 4956

Added a beta distribution model

243 lines of code changed in 3 files:

msuchard 2012-05-15 01:24 Rev.: 4955

Introduced a trial TreeParameterModel that excludes external branches; created a new branch-specific Pagel estimator

165 lines of code changed in 6 files:

fbielejec 2012-05-12 01:55 Rev.: 4954

working on parser

23 lines of code changed in 1 file:

fbielejec 2012-05-11 20:37 Rev.: 4953

working on parser

48 lines of code changed in 3 files:

msuchard 2012-05-11 16:02 Rev.: 4952

Trying a tree transform

100 lines of code changed in 4 files:

msuchard 2012-05-11 15:19 Rev.: 4951

Refactoring TransformedTree to make generalizations easier

144 lines of code changed in 4 files:

msuchard 2012-05-11 11:24 Rev.: 4950

Hopefully resolves issue 618. Codon-partitioned models do not throw XML errors with ancestral sequence reconstruction. There is still an issue with the "count" parameter name for non-dNdS robust counting. So, non-dNdS robust counting is temporarily disabled for CP models.

127 lines of code changed in 3 files:

msuchard 2012-05-11 09:04 Rev.: 4949

Resolved XML problem with ancestral reconstruction for MRCA that were not the root.

2 lines of code changed in 1 file:

mandevsgill 2012-05-11 07:21 Rev.: 4948

Correct version of GMRF multilocus likelihood

268 lines of code changed in 1 file:

graham853@gmail.com 2012-05-10 00:51 Rev.: 4946

Extending allopolyploid model to deal with arbitrary numbers of diploids. Most new code is in new class AlloppDiploidHistory and old class AlloppNetworkNodeSlide.

2353 lines of code changed in 13 files:

fbielejec 2012-05-09 02:17 Rev.: 4945

epoch model simulation

5 lines of code changed in 1 file:

fbielejec 2012-05-09 01:30 Rev.: 4944

epoch model simulation

21 lines of code changed in 1 file:

fbielejec 2012-05-08 04:16 Rev.: 4943

parser for beagle simulator

4 lines of code changed in 1 file:

fbielejec 2012-05-08 02:09 Rev.: 4942

working on epoch model simulation

21 lines of code changed in 1 file:

fbielejec 2012-05-08 00:20 Rev.: 4941

homogenous simulation

42 lines of code changed in 1 file:

fbielejec 2012-05-07 20:51 Rev.: 4940

working on beagle simulator

67 lines of code changed in 1 file:

fbielejec 2012-05-06 23:25 Rev.: 4939

parser for beagle simulator

255 lines of code changed in 2 files:

fbielejec 2012-05-06 23:14 Rev.: 4938

parser for beagle simulator

144 lines of code changed in 2 files:

fbielejec 2012-05-06 10:48 Rev.: 4937

working on beagle simulator

4 lines of code changed in 1 file:

fbielejec 2012-05-06 08:41 Rev.: 4936

working on beagle simulator

55 lines of code changed in 1 file:

sibon.li 2012-05-04 10:46 Rev.: 4935

Fixed AncestralSequenceAnnotator to use KALIGN instead of CLUSTAL (much faster)

17 lines of code changed in 1 file:

fbielejec 2012-05-04 00:27 Rev.: 4934

working on BEAGLE seq simulator

193 lines of code changed in 1 file:

April 2012 »

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