November 2009 Commit Log

Number of Commits:
69
Number of Active Developers:
8
rambaut 2009-11-30 23:58 Rev.: 2635

Work on next version of Tracer. Implemented a 'GMRF Skyride' analysis. Implemented feature request <http://code.google.com/p/beast-mcmc/issues/detail?id=191> to display burnins in different colour.

842 lines of code changed in 11 files:

msuchard 2009-11-30 08:34 Rev.: 2626

MarkovJumps now processes multiple register matrices at a time

121 lines of code changed in 4 files:

rambaut 2009-11-29 08:53 Rev.: 2625

New version of Path-O-Gen v1.2 released.

236 lines of code changed in 8 files:

msuchard 2009-11-27 08:43 Rev.: 2620

Smashing bugs in MarkovJumps

39 lines of code changed in 3 files:

msuchard 2009-11-27 06:24 Rev.: 2619

Smashing bugs in MarkovJumps

23 lines of code changed in 2 files:

rambaut 2009-11-27 03:59 Rev.: 2617

Removed a warning that is no longer valid.

3 lines of code changed in 1 file:

rambaut 2009-11-26 11:55 Rev.: 2615

Refactoring work on SPREAD

1278 lines of code changed in 28 files:

rambaut 2009-11-26 05:24 Rev.: 2613

SPREAD...

219 lines of code changed in 6 files:

rambaut 2009-11-26 04:04 Rev.: 2612

Another little tree processing main.

308 lines of code changed in 3 files:

rambaut 2009-11-26 03:34 Rev.: 2610

Added icons to the SPREAD data table.

424 lines of code changed in 15 files:

rambaut 2009-11-26 02:58 Rev.: 2608

A bug in BeastDialog would have caused a null pointer exception whenever it was used. Good thing I tested it.

18 lines of code changed in 2 files:

msuchard 2009-11-25 17:43 Rev.: 2607

Fixed MarkovJumps to work when mutation rate is specified in siteModel

132 lines of code changed in 5 files:

msuchard 2009-11-25 15:17 Rev.: 2602

Small test file for MarkovJumps

102 lines of code changed in 1 file:

msuchard 2009-11-25 13:49 Rev.: 2597

Interfacing markovjumps to a TreeLikelihood for jump reconstruction

267 lines of code changed in 10 files:

rambaut 2009-11-25 13:36 Rev.: 2596

SPREAD continues to develop

787 lines of code changed in 10 files:

philippe.lemey@gmail.com 2009-11-24 11:40 Rev.: 2591

DiscreteRatePriorGenerator tweaks

1 lines of code changed in 1 file:

msuchard 2009-11-24 11:08 Rev.: 2590

Tested alignment statistics; appear fine.

27 lines of code changed in 2 files:

mtholder 2009-11-24 06:52 Rev.: 2587

This commit adds a script and template files to the plugins_SDK directory (no
changes to java source code in BEAST). The directory now contains a simple
python script that will create a stub for a BEAST plugin. This is primarily a
matter of copying some file templates and changing names to the name that the
plugin author chooses). The plugins_SDK/README describes how the script should
be used. In addition to creating source code stubs, the generate_stub.py script
will creat an ant file with appropriate targets and a simple XML instance
document that uses an new XML element (that the plugin must parse).

Most of this code was written at the NESCent BEAST working group. Version
control for earlier versions of this is via git at
git@github.com:mtholder/beastPlugin.git


738 lines of code changed in 8 files:

rambaut 2009-11-24 05:11 Rev.: 2586

Implemented more alignment stats in BasicAlignment.toString(). A site is considered informative if at least 2 states are observed at least 2 times. A site is considered a singleton if it is not conserved and not informative.

65 lines of code changed in 1 file:

philippe.lemey@gmail.com 2009-11-24 04:40 Rev.: 2585

DiscreteRatePriorGenerator tweaks

1009 lines of code changed in 1 file:

rambaut 2009-11-24 03:18 Rev.: 2583

Added commandline option to TreeLogAnalyser to set credible set probability cutoff.

15 lines of code changed in 1 file:

msuchard 2009-11-23 13:38 Rev.: 2579

BEAST now counts number of invariant sites

13 lines of code changed in 2 files:

rambaut 2009-11-22 12:41 Rev.: 2578

Work progressing on SPREAD. Doesn't do anything useful yet but compiles and runs.

221 lines of code changed in 30 files:

msuchard 2009-11-22 05:13 Rev.: 2577

Refactoring markovjumps into a core and a wrapper

470 lines of code changed in 6 files:

msuchard 2009-11-21 14:27 Rev.: 2576

Started implementing Markov chain-induced counting processes in BEAST

282 lines of code changed in 1 file:

rambaut 2009-11-20 05:10 Rev.: 2566

More slow, steady progress for 'SPREAD'.

149 lines of code changed in 7 files:

msuchard 2009-11-19 08:30 Rev.: 2553

Standardizing output between different CSM implementations

35 lines of code changed in 3 files:

msuchard 2009-11-19 08:23 Rev.: 2552

Yet more bug fixes in Beagle.ComplexSubstitutionModel

6 lines of code changed in 2 files:

bloomquist 2009-11-19 07:39 Rev.: 2551

A few of the classes were using TREE_FILE_NAME string from some of the classes I deleted. I moved this String into STARBEASTOptions and made the appropriate changes. I don't think BEAST will be broken anymore after this.

15 lines of code changed in 3 files:

msuchard 2009-11-19 07:29 Rev.: 2550

Small bug fixed

3 lines of code changed in 1 file:

msuchard 2009-11-19 07:05 Rev.: 2549

Compilation bugs

2 lines of code changed in 2 files:

bloomquist 2009-11-19 06:09 Rev.: 2548

Removed some obsolete classes from the dr.evomodel.coalescent package. These were loggers that were used to obtain the population sizes at fixed points in time. The use of a simple statistic however, is much easier and fits into logging framework in a smooth fashion. Thus, I have decided to tame the beast and remove some extraneous code. If these are needed at a later date, one can always check out a previous revision.

Have also updated the release_parsers.properties to remove these parsers.

3 lines of code changed in 6 files:

rambaut 2009-11-19 05:02 Rev.: 2547

More slow, steady progress for 'SPREAD'.

12 lines of code changed in 1 file:

rambaut 2009-11-19 04:45 Rev.: 2546

More slow, steady progress for 'SPREAD'.

362 lines of code changed in 11 files:

msuchard 2009-11-17 17:29 Rev.: 2541

Static rescaling (turned on after first under/over-flow appears to be working.

1 lines of code changed in 1 file:

bloomquist 2009-11-17 14:53 Rev.: 2540

Added in a statistic for the Generalized Skyline. The statistic returns the time slice of the the skyline for a given time. If the time is beyond the root height, the statistic return Double.NaN.

76 lines of code changed in 2 files:

jheled 2009-11-17 12:07 Rev.: 2539

Initial fix for issue 248 (still no user visible message)

27 lines of code changed in 1 file:

rambaut 2009-11-17 05:16 Rev.: 2538

SPREADing nutella...

608 lines of code changed in 5 files:

msuchard 2009-11-17 04:53 Rev.: 2537

Trying to add support for old-school static rescaling (after first underflow). Could use some help from Andrew.

44 lines of code changed in 3 files:

rambaut 2009-11-13 01:32 Rev.: 2534

New library to add to the project. Only required for dr.app.phylogeography.* so either exclude this from your build or add kmlframework_20090320.jar to your libraries.

0 lines of code changed in 1 file:

rambaut 2009-11-13 01:28 Rev.: 2533

More SPREAD work.

586 lines of code changed in 7 files:

msuchard 2009-11-12 05:49 Rev.: 2531

Fixed in case users wrap a parameter in a column and forget to provide a label

1 lines of code changed in 1 file:

msuchard 2009-11-12 03:22 Rev.: 2530

Attacking the wandering taxon problem

118 lines of code changed in 3 files:

msuchard 2009-11-11 15:00 Rev.: 2529

Empiricial distributions can now take an offset in the <data> block

17 lines of code changed in 4 files:

rambaut 2009-11-11 01:25 Rev.: 2528

Starting to add structure to the phylogeography GUI.

546 lines of code changed in 9 files:

rambaut 2009-11-11 00:06 Rev.: 2527

Added a new GUI-based phylogeography reconstruction application. This is not close to working yet but compiles.

1475 lines of code changed in 22 files:

alexei.drummond 2009-11-10 11:42 Rev.: 2525

small code changes for binary covarion model

94 lines of code changed in 4 files:

dong.w.xie 2009-11-09 16:42 Rev.: 2521

Trunk: merge the parsers change from branch 1.5 into trunk.

51 lines of code changed in 3 files:

alexei.drummond 2009-11-09 14:17 Rev.: 2519

1138 lines of code changed in 12 files:

msuchard 2009-11-07 10:28 Rev.: 2515

Testing out random effects for GLM substitution models. Added GLM substitution models to BEAGLE.

155 lines of code changed in 6 files:

rambaut 2009-11-06 08:39 Rev.: 2513

Added a metropolisHastings option to the EmpiricalTreeDistributionOperator

17 lines of code changed in 4 files:

msuchard 2009-11-05 18:17 Rev.: 2512

Implemented random effects in generalized linear regression models (primarily for phylogeographic model fitting)

61 lines of code changed in 3 files:

msuchard 2009-11-05 13:23 Rev.: 2511

Removed code duplication in determining if a nasty substitution model is connected and well-conditioned.

78 lines of code changed in 8 files:

msuchard 2009-11-05 07:53 Rev.: 2509

Making BEAGLE ComplexSubstitutionModel as compatible with the old CSM as possible. Removing duplicated code in SVSCSMParser.

108 lines of code changed in 3 files:

rambaut 2009-11-05 03:21 Rev.: 2507

A fix for the empiricalTreeDistributionModel. If the NEXUS tree file uses a translation list then these numbers are used as node numbers.

44 lines of code changed in 2 files:

alexei.drummond 2009-11-04 15:18 Rev.: 2505

LineagesThroughTimeDialog now reports 1 lineage for times above the root of a tree. This is nicer than the conditional version when comparing against known analytical results for lineage through time plots.

3 lines of code changed in 1 file:

dong.w.xie 2009-11-04 14:39 Rev.: 2502

Fix trunk bug of parser loading in r2496

10 lines of code changed in 1 file:

msuchard 2009-11-04 14:12 Rev.: 2500

Still some pesky errors with the conversion from Parameters to Variables

3 lines of code changed in 1 file:

dong.w.xie 2009-11-04 10:54 Rev.: 2496

To solve release parser out of date problem:
1) Always load release_parser.properties;
2) development_parser.properties should contain additional parsers only available for development, which should NOT duplicate with release parsers;
3) add WARNING message to check the dulication of parser loading.

182 lines of code changed in 3 files:

rambaut 2009-11-03 01:42 Rev.: 2494

TimeSlicer now writes out calendar dates (yyyy-MM-dd) as required by the KML format.

357 lines of code changed in 1 file:

rambaut 2009-11-02 21:57 Rev.: 2493

Adjusted the performance measurement delay in logger to be a fixed 10,000 steps (should avoid the full evaluation test period).

3 lines of code changed in 2 files:

dong.w.xie 2009-11-02 16:29 Rev.: 2492

a covinient change for the release

1 lines of code changed in 2 files:

dong.w.xie 2009-11-02 15:48 Rev.: 2491

Further improvement of BEAST parser doc

2 lines of code changed in 1 file:

dong.w.xie 2009-11-02 11:02 Rev.: 2490

sovle Issue 229: Another failure of testing framework

6 lines of code changed in 2 files:

dong.w.xie 2009-11-02 10:47 Rev.: 2489

Making better BeastParserDoc.

213 lines of code changed in 4 files:

jheled 2009-11-01 14:22 Rev.: 2488

eigen values (in comment only, until the correct magnitude, order and orientation is verified)

32 lines of code changed in 1 file:

jheled 2009-11-01 14:20 Rev.: 2487

code police

8 lines of code changed in 1 file:

jheled 2009-11-01 14:20 Rev.: 2486

generify

29 lines of code changed in 5 files:

jheled 2009-11-01 10:07 Rev.: 2485

fix problem with array attributes. Change burnin to be in number of trees like the rest of BEAST.

19 lines of code changed in 1 file:

October 2009 »

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