April 2011 Commit Log

Number of Commits:
52
Number of Active Developers:
5
msuchard 2011-04-29 10:18 Rev.: 3968

Uniformized simulation now falls back on rejection sampling when numerically instable.

74 lines of code changed in 6 files:

rambaut 2011-04-29 01:36 Rev.: 3967

Allow treelogger to have more than one trait filter (comma or space delimited).

10 lines of code changed in 1 file:

dong.w.xie 2011-04-28 15:46 Rev.: 3966

Trunk: solve Issue 456: correct *BEAST tutorial

529 lines of code changed in 2 files:

dong.w.xie 2011-04-28 14:57 Rev.: 3965

Trunk: solve Issue 455: BEAUti: If a trait has its name changed, the values are deleted

7 lines of code changed in 1 file:

rambaut 2011-04-28 04:27 Rev.: 3964

5 lines of code changed in 2 files:

dong.w.xie 2011-04-27 16:07 Rev.: 3963

Trunk: solve Issue 454: BEAUti: all the taxon sets are deleted when link/unlink tree

7 lines of code changed in 1 file:

msuchard 2011-04-27 15:50 Rev.: 3962

Added logging ability for complete substitution history under uniformization; there is a high likelihood that I broke some of the Markov jumps/reward mechanisms in this update.

308 lines of code changed in 11 files:

rambaut 2011-04-27 02:23 Rev.: 3960

28 lines of code changed in 1 file:

akaruiws 2011-04-26 14:48

0 lines of code changed in 2 files:

rambaut 2011-04-26 04:21 Rev.: 3956

Work on TreeSpace.

176 lines of code changed in 5 files:

rambaut 2011-04-25 23:56 Rev.: 3955

TreeSpace...

129 lines of code changed in 3 files:

rambaut 2011-04-23 04:04 Rev.: 3954

58 lines of code changed in 3 files:

rambaut 2011-04-23 01:29 Rev.: 3953

TreeSpace...

37 lines of code changed in 2 files:

rambaut 2011-04-22 04:30 Rev.: 3952

Work on TreeSpace.

174 lines of code changed in 3 files:

rambaut 2011-04-22 03:00 Rev.: 3951

Fixed a parser that allows you to create patterns of constant sites which can then me merged with polymorphic sites to reconstruct a full pattern set.

3 lines of code changed in 1 file:

rambaut 2011-04-22 02:59 Rev.: 3950

Work on TreeSpace app

337 lines of code changed in 6 files:

dong.w.xie 2011-04-21 18:20 Rev.: 3949

tutorial update

0 lines of code changed in 10 files:

dong.w.xie 2011-04-21 18:08

tutorial update

0 lines of code changed in 4 files:

dong.w.xie 2011-04-21 18:03 Rev.: 3944

tutorial update BSP

6877 lines of code changed in 22 files:

dong.w.xie 2011-04-21 17:00 Rev.: 3943

tutorial update

9106 lines of code changed in 24 files:

rambaut 2011-04-20 22:28 Rev.: 3942

Another tweak to the previous fix for issue 436 - the sequence error model combo now shows "Off" when disabled.

6 lines of code changed in 1 file:

rambaut 2011-04-20 22:25 Rev.: 3941

A tweak to the previous fix for issue 436 - ensure that the sequence error model doesn't generate if there is not exactly 1 data partition.

18 lines of code changed in 1 file:

rambaut 2011-04-20 21:13 Rev.: 3940

Second part of fix for issue 436 (http://code.google.com/p/beast-mcmc/issues/detail?id=436) - Sequence Error Model is disabled when multiple partitions are being used. Tool tip explains why it is disabled.

22 lines of code changed in 1 file:

rambaut 2011-04-20 20:49 Rev.: 3939

First part of a fix for issue 436 (http://code.google.com/p/beast-mcmc/issues/detail?id=436): This will prevent a TipPartialsModel being reused for different PatternLists.

7 lines of code changed in 1 file:

dong.w.xie 2011-04-20 17:58 Rev.: 3938

tutorial figures

825 lines of code changed in 7 files:

dong.w.xie 2011-04-20 16:56 Rev.: 3937

Trunk: update /doc/tutorial.

585 lines of code changed in 1 file:

dong.w.xie 2011-04-20 16:43 Rev.: 3936

Trunk: add tutorials in /doc/tutorial.

1032 lines of code changed in 102 files:

msuchard 2011-04-16 02:27 Rev.: 3935

Missing data registry entry for co-evolution amino acid sites

2 lines of code changed in 1 file:

dong.w.xie 2011-04-15 16:23 Rev.: 3934

Trunk: xml example = testCoalescent1.xml in BEAST 2.

213 lines of code changed in 1 file:

msuchard 2011-04-15 08:03 Rev.: 3933

Fixing indicator randomization for reversible models

27 lines of code changed in 4 files:

dong.w.xie 2011-04-11 12:39 Rev.: 3932

Trunk: fix a bug of the new XML for Calibration with Yule.

18 lines of code changed in 1 file:

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

Work on dependent evolution between pairs of amino acids

339 lines of code changed in 4 files:

msuchard 2011-04-10 03:58 Rev.: 3930

Updated compileNativeMacOSX.sh to work under 10.6 and added a parse class for paired-amino acid evolution

145 lines of code changed in 2 files:

akaruiws 2011-04-09 19:19 Rev.: 3929

Change the performance suggestion.

5 lines of code changed in 1 file:

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

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

125 lines of code changed in 6 files:

jheled 2011-04-07 09:23 Rev.: 3927

Correctly handle calibration on root

14 lines of code changed in 1 file:

rambaut 2011-04-07 03:25 Rev.: 3926

Removed a redundant parser reference

0 lines of code changed in 1 file:

akaruiws 2011-04-04 10:17 Rev.: 3925

Correct tag name.

2 lines of code changed in 2 files:

dong.w.xie 2011-04-02 13:35 Rev.: 3924

fix JUnit test as Jessie advised

4 lines of code changed in 1 file:

rambaut 2011-04-01 21:00 Rev.: 3923

Added Tanja's paper back to the Yule citation.

3 lines of code changed in 1 file:

rambaut 2011-04-01 20:42 Rev.: 3922

Added reference for Yule model if we are going to be complete. Should we also cite Gernhard, T., 2008 or is this distribution the same when death rate=0?

5 lines of code changed in 1 file:

akaruiws 2011-04-01 18:56 Rev.: 3921

Tidy up more msatBMA related things.

73 lines of code changed in 6 files:

dong.w.xie 2011-04-01 17:53 Rev.: 3920

Trunk: A new XML for Calibration with Yule.

82 lines of code changed in 8 files:

dong.w.xie 2011-04-01 17:14 Rev.: 3919

Trunk: fix a bug on operator generator

2 lines of code changed in 1 file:

dong.w.xie 2011-04-01 13:20 Rev.: 3918

Trunk: finish micro-sat finailly.

90 lines of code changed in 2 files:

dong.w.xie 2011-04-01 11:30 Rev.: 3917

Trunk: fix build.

2 lines of code changed in 1 file:

dong.w.xie 2011-04-01 11:25 Rev.: 3916

Trunk: solve Issue 447: The Birth-Death models in the Trees Panel show a citation - other models do not.

72 lines of code changed in 2 files:

dong.w.xie 2011-04-01 09:52 Rev.: 3915

Trunk: solve Issue 449: BEAUti: Bayesian Skyline should be removed for multi-tree.

19 lines of code changed in 2 files:

akaruiws 2011-04-01 09:47 Rev.: 3914

Correcting according to changes made to the models.

3 lines of code changed in 2 files:

dong.w.xie 2011-04-01 09:22 Rev.: 3913

Trunk: fix a small bug.

1 lines of code changed in 1 file:

rambaut 2011-04-01 03:06 Rev.: 3912

Added citations for other tree prior models (ESBP still needs to be added - sorry, I couldn't find it quick enough).

20 lines of code changed in 1 file:

akaruiws 2011-04-01 01:16 Rev.: 3911

Tidy up MsatBMA related things.

739 lines of code changed in 13 files:

March 2011 »

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