September 2010 Commit Log

Number of Commits:
90
Number of Active Developers:
8
alexei.drummond 2010-09-29 21:34 Rev.: 3587

Added the sampling of the origin of the infection to the birth-death serial sampling model.

2 lines of code changed in 1 file:

alexei.drummond 2010-09-29 19:02 Rev.: 3586

Added the sampling of the origin of the infection to the birth-death serial sampling model.

1 lines of code changed in 1 file:

alexei.drummond 2010-09-29 18:56 Rev.: 3585

Added the sampling of the origin of the infection to the birth-death serial sampling model.

41 lines of code changed in 2 files:

msuchard 2010-09-28 13:45 Rev.: 3584

Fixed bug in LogCombiner, such that Tracer choked when trying to read combined logs with very large state numbers

29 lines of code changed in 2 files:

msuchard 2010-09-28 09:02 Rev.: 3583

Getting aggressive with fixing zero-branch-lengths in starting trees; need comparison of why MutableTree.Utils is not working

59 lines of code changed in 2 files:

msuchard 2010-09-28 06:44 Rev.: 3582

Fixed GeneralSubstitutionModelParser when relativeTo is not provided.

2 lines of code changed in 2 files:

jheled 2010-09-27 17:57 Rev.: 3580

Now that times() is used to print values in log, change implementation to return only the externally visible ones.

2 lines of code changed in 2 files:

dong.w.xie 2010-09-27 13:49 Rev.: 3578

Trunk: tidy up JUnit test in app

578 lines of code changed in 7 files:

dong.w.xie 2010-09-27 12:03 Rev.: 3577

Trunk: change JDK1.6 code Arrays.copyOf to JDK1.5 code System.arraycopy

6 lines of code changed in 1 file:

alexei.drummond 2010-09-27 11:44

Changed species tree annotations to use two double arrays: dmt and dmv to represent the times and values of the demographic function for the associated branch. This fits in with standard TreeTrait.DA() class and will be automatically annotated by TreeAnnotator and visualizable in FigTree. Some changes in *BEAST specific post-processing will be necessary but I don't have access to that code which I believe is in Python somewhere.

396 lines of code changed in 4 files:

rambaut 2010-09-27 11:01 Rev.: 3574

A fix for issue 407 <http://code.google.com/p/beast-mcmc/issues/detail?id=407>. Wrap the return string value from the VDemographicFunction.toString() in the '{...}' expected by TreeAnnotator.

1 lines of code changed in 1 file:

msuchard 2010-09-27 09:25 Rev.: 3573

TreeLoggerParser can now filter which tree traits to report.

23 lines of code changed in 1 file:

akaruiws 2010-09-25 18:02 Rev.: 3572

updates for watkins msat model classes.

117 lines of code changed in 3 files:

alexander.alekseyenko 2010-09-25 04:58 Rev.: 3571

Started MV Polya Likelihood model

343 lines of code changed in 6 files:

jheled 2010-09-24 13:14 Rev.: 3570

Catch errors which lead to beast infinite loop or failure in parsers. more detailed error messages.

18 lines of code changed in 8 files:

dong.w.xie 2010-09-24 10:41 Rev.: 3569

Trunk: more JUnit tests

103 lines of code changed in 3 files:

dong.w.xie 2010-09-24 10:38 Rev.: 3568

Trunk: active a JUnit test

269 lines of code changed in 2 files:

alexander.alekseyenko 2010-09-24 04:20 Rev.: 3567

fix and move a few example files of my making

249 lines of code changed in 10 files:

alexander.alekseyenko 2010-09-24 04:19 Rev.: 3566

add a new operator on sum constrained parameter, providing better mixing for multiscale parameters

216 lines of code changed in 3 files:

akaruiws 2010-09-23 20:13

Simulator for geographic locations by homogeneous diffusion.

121 lines of code changed in 3 files:

dong.w.xie 2010-09-23 16:18 Rev.: 3563

Trunk: merge issue 404 from branch 1.6

3 lines of code changed in 1 file:

dong.w.xie 2010-09-22 12:54 Rev.: 3561

Trunk: merge issue 399 from branch 1.6

10 lines of code changed in 5 files:

philippe.lemey@gmail.com 2010-09-18 01:11 Rev.: 3556

added an optoin to specify the bivariate HPD interval in TreeAnnotator (command line)

16 lines of code changed in 1 file:

dong.w.xie 2010-09-17 12:23 Rev.: 3555

Trunk: merge *BEAST bug fix from branch 1.6

94 lines of code changed in 2 files:

dong.w.xie 2010-09-15 16:50 Rev.: 3549

Trunk: delete since Intellj problem

0 lines of code changed in 1 file:

dong.w.xie 2010-09-15 16:28 Rev.: 3547

Trunk: fix build bug maing release failed

26 lines of code changed in 6 files:

dong.w.xie 2010-09-15 11:48 Rev.: 3542

Trunk: update Version number and history

12 lines of code changed in 2 files:

dong.w.xie 2010-09-15 10:45 Rev.: 3541

Trunk: solve Issue 396: make alias "forParent" of "includeStem" in TMRCAPasrer

27 lines of code changed in 4 files:

msuchard 2010-09-15 07:58 Rev.: 3540

Fixed ComplexSubstitutionModel so that pi parameter does post-multiply the rates parameter.

7 lines of code changed in 1 file:

dong.w.xie 2010-09-14 18:11 Rev.: 3539

Trunk: solve Issue 394: Beuati fails to guess species names

2 lines of code changed in 1 file:

dong.w.xie 2010-09-14 11:03 Rev.: 3538

Trunk: solve Issue 395: BEAUti: *BEAST check box should be unchecked after all data partition is deteled

3 lines of code changed in 1 file:

rambaut 2010-09-13 22:26 Rev.: 3537

Renamed TreeDispersionStatistic to DiffusionRateStatistic to be more consistent with other terminology. The former name is still recognized as a synonym.

130 lines of code changed in 3 files:

rambaut 2010-09-13 22:13 Rev.: 3536

Added a link to Philippe's new continuous diffusion tutorials.

2 lines of code changed in 1 file:

philippe.lemey@gmail.com 2010-09-13 22:00

updated continuous phylogeography xml examples

0 lines of code changed in 4 files:

rambaut 2010-09-13 21:47 Rev.: 3532

Added a link to Philippe's new continuous diffusion tutorials.

2 lines of code changed in 1 file:

philippe.lemey@gmail.com 2010-09-13 21:47 Rev.: 3533

updated continuous phylogeography xml examples

0 lines of code changed in 2 files:

dong.w.xie 2010-09-13 15:47 Rev.: 3531

Trunk: new change of BirthDeathSerialSamplingModel

16 lines of code changed in 3 files:

dong.w.xie 2010-09-13 11:58 Rev.: 3530

Trunk: correction of r3529

4 lines of code changed in 1 file:

dong.w.xie 2010-09-13 10:51 Rev.: 3529

Trunk: solve Issue 393: Fix the message of the Bayes factor report in Tracer

3 lines of code changed in 1 file:

msuchard 2010-09-13 07:07 Rev.: 3528

Made logging of multilocus GMRF skyride more convenient for plotting in Tracer:
<log id="skyrideLog" logEvery="5000" fileName="multilocusGMRF-skyride.log">
<parameter idref="skyride.logPopSize"/>
<gmrfHeightsStatistic id="skyride.intervalHeights">
<gmrfSkyrideLikelihood idref="skyrideCoalescent"/>
</gmrfHeightsStatistic>
</log>

113 lines of code changed in 3 files:

rambaut 2010-09-11 08:41 Rev.: 3527

Fixed issue 369: http://code.google.com/p/beast-mcmc/issues/detail?id=369

6 lines of code changed in 1 file:

rambaut 2010-09-11 01:58 Rev.: 3526

Fixed an issue with UPGMA producing zero internal branch lengths and causing zero probability in some tree priors.

76 lines of code changed in 3 files:

msuchard 2010-09-11 00:27 Rev.: 3525

Changing default BEAST behavior to throw exception if BEAGLE not found, instead of trying to run the Java BEAGLE implementation that is incomplete and crashes anyway.

0 lines of code changed in 1 file:

rambaut 2010-09-10 21:12 Rev.: 3524

TreeDispersionStatistic doesn't need a TreeModel as it can extract this from the AbstractMultivariateTreeLikelihood(s). It shouldn't be a TreeStatistic because it can't provide the value for an arbitrary tree.

21 lines of code changed in 1 file:

dong.w.xie 2010-09-10 17:15 Rev.: 3523

Trunk: update Version History

19 lines of code changed in 1 file:

dong.w.xie 2010-09-10 16:55 Rev.: 3522

Trunk: solve Issue 337: Creating a 'CONTINUOUS' or 'INTEGER' trait gives Discrete model of substitution in SiteModelPanel

8 lines of code changed in 1 file:

dong.w.xie 2010-09-10 16:29 Rev.: 3521

Trunk: solve Issue 382: Minor Typo in Treestat, and update Version history

2 lines of code changed in 3 files:

rambaut 2010-09-10 03:17 Rev.: 3520

Forgot to actually implement the swap.

5 lines of code changed in 3 files:

rambaut 2010-09-10 03:01 Rev.: 3519

Modification of TreeDispersionStatistic to take multiple AbstractMultivariateTraitLikelihood and average the statistic across all the branches in all the trees (for joint estimation from independent trees).

32 lines of code changed in 1 file:

rambaut 2010-09-10 02:54 Rev.: 3518

Implemented an operator to swap tip trait values in an IntegratedMultivariateTraitLikelihood (yes Marc, I do need to do this).

126 lines of code changed in 3 files:

rambaut 2010-09-09 23:49 Rev.: 3517

Now I really think it builds OK. Sorry if anyone got messed up by that.

173 lines of code changed in 1 file:

rambaut 2010-09-09 23:38 Rev.: 3516

Now I think it builds OK. Sorry if anyone got messed up by that.

1 lines of code changed in 2 files:

rambaut 2010-09-09 23:33 Rev.: 3515

A few more bits of clean up.

4 lines of code changed in 7 files:

rambaut 2010-09-09 23:27 Rev.: 3514

I forgot to change the package locations of some files copied in from elsewhere

77 lines of code changed in 36 files:

rambaut 2010-09-09 23:01

569 lines of code changed in 18 files:

dong.w.xie 2010-09-09 14:25 Rev.: 3511

Trunk: solve Issue 322: Tracer: stack buttons to save space

29 lines of code changed in 1 file:

dong.w.xie 2010-09-09 12:38 Rev.: 3510

Trunk: solve Issue 392: BEAUti: wrong validation to apply Normal prior to tmrca

2 lines of code changed in 1 file:

dong.w.xie 2010-09-09 11:45 Rev.: 3509

Trunk: Issue 363: Add tooltips for all UI elements

55 lines of code changed in 3 files:

msuchard 2010-09-09 04:22 Rev.: 3508

Better checking in generalized linear models to ensure that design matrices are of full rank.

64 lines of code changed in 6 files:

dong.w.xie 2010-09-08 11:02 Rev.: 3507

Trunk: update Version History

4 lines of code changed in 1 file:

msuchard 2010-09-08 10:34 Rev.: 3506

Improved store/restore functionality in GMRF multilocus model.

61 lines of code changed in 4 files:

akaruiws 2010-09-08 10:06 Rev.: 3505

Added methods for computing the transition probabilities.

11 lines of code changed in 3 files:

akaruiws 2010-09-08 09:52 Rev.: 3504

Added methods for computing the transition probabilities.

35 lines of code changed in 1 file:

akaruiws 2010-09-08 00:43 Rev.: 3503

New msat model described by Watkins (2007).

22 lines of code changed in 1 file:

alexei.drummond 2010-09-07 23:08 Rev.: 3502


49 lines of code changed in 1 file:

dong.w.xie 2010-09-07 17:32 Rev.: 3501

Trunk: solve Issue 391: BEAUti: add forParent for taxon set

32 lines of code changed in 3 files:

dong.w.xie 2010-09-07 16:35 Rev.: 3500

Trunk: solve Issue 387: BEAUti generates wrong xml when a uniform prior is selected fo species.popMean

2 lines of code changed in 1 file:

dong.w.xie 2010-09-07 15:19 Rev.: 3499

Trunk: solve Issue 389: add TreeStat into BEAST release

109 lines of code changed in 5 files:

dong.w.xie 2010-09-07 11:57 Rev.: 3498

Trunk: correct new update of BirthDeathSerialSamplingModel

23 lines of code changed in 3 files:

rambaut 2010-09-07 10:37 Rev.: 3497

Switched all uses of org.virion.jam.* to jam.* (org.virion.jam.* is not being updated or fixed). This has touched alot of files but mainly just in the import statements.

9503 lines of code changed in 256 files:

dong.w.xie 2010-09-06 18:07 Rev.: 3496

Trunk: add a comment

1 lines of code changed in 1 file:

dong.w.xie 2010-09-06 17:03 Rev.: 3495

Trunk: solve Issue 386: xml file name should be shown in BEAST window

14 lines of code changed in 1 file:

dong.w.xie 2010-09-06 16:47 Rev.: 3494

Trunk: solve Issue 385: Warning message of using random local clock model

2 lines of code changed in 1 file:

dong.w.xie 2010-09-06 16:42 Rev.: 3493

Trunk: update version history

44 lines of code changed in 1 file:

dong.w.xie 2010-09-06 15:37 Rev.: 3492

Trunk: update BirthDeathSerialSamplingModel logL

24 lines of code changed in 3 files:

dong.w.xie 2010-09-06 15:33 Rev.: 3491

Trunk: solve Issue 388: BEAUti: "species" should NOT be used as a trait name

18 lines of code changed in 2 files:

philippe.lemey@gmail.com 2010-09-04 07:57 Rev.: 3490

marc did something

46 lines of code changed in 1 file:

philippe.lemey@gmail.com 2010-09-04 07:55 Rev.: 3489

adding the ability to consider unions of polygons in GeoSpatialCollection

1 lines of code changed in 1 file:

msuchard 2010-09-04 04:08 Rev.: 3488

Removed duplicated code in GMRFMultilocusSkyrideLikelihood and added option in GMRFSkyride to not scale by rootHeight; turning this latter option off is for debugging only

79 lines of code changed in 9 files:

msuchard 2010-09-04 04:04 Rev.: 3487

Add several wrappers to convert automatically between different reductions of TreeTraits (sum over tree, sum across sites, etc.). One can even double-wrap to get sum over tree + sum across sites. This should reduce substantial code-duplication and earn me a gold star.

1310 lines of code changed in 7 files:

dong.w.xie 2010-09-03 14:36 Rev.: 3486

Trunk: solve Issue 384: Unhandled attribute (typo?) name in sumStatistic:rateChanges

3 lines of code changed in 1 file:

dong.w.xie 2010-09-03 14:29 Rev.: 3485

Trunk: solve Issue 377: BEAUti: Random local clock model Bug

169 lines of code changed in 6 files:

dong.w.xie 2010-09-03 14:02 Rev.: 3484

Trunk: solve Issue 381: Discrete trait model can select an inappropriate substitution model in the data partition table

54 lines of code changed in 2 files:

dong.w.xie 2010-09-02 11:57 Rev.: 3483

Trunk: solve Issue 383: BEAUti: "species" trait should not appear in Data Panel

13 lines of code changed in 2 files:

rambaut 2010-09-02 04:07 Rev.: 3482

Fixed an error when generating starting tree for multiple sequence data partitions and a discrete trait partition - the generator was checking alignments but the discrete trait partition doesn't have one.

28 lines of code changed in 1 file:

rambaut 2010-09-02 03:37 Rev.: 3481

Grammatical corrections.

18 lines of code changed in 1 file:

rambaut 2010-09-02 02:22 Rev.: 3480

Fixed a few issues with SequenceErrorModel. Also added an automatic dimension setting for the popsize parameter in GMRF.

40 lines of code changed in 3 files:

rambaut 2010-09-02 01:35 Rev.: 3479

Added an optional indicator parameter into the sequence error model to try to identify damaged sequences.

120 lines of code changed in 3 files:

dong.w.xie 2010-09-01 16:56 Rev.: 3478

Trunk: solve Issue 380: Discrete trait model should have its tree linked to that for a tree for a sequence partition

7 lines of code changed in 2 files:

rambaut 2010-09-01 10:45 Rev.: 3477

Fixed issue where pressing "Guess Traits" to create a new trait resulted in the Guess Traits Dialog appearing twice.

9 lines of code changed in 3 files:

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