November 2011 Commit Log

Number of Commits:
111
Number of Active Developers:
8
dong.w.xie 2011-11-30 10:53 Rev.: 4497

trunk:solve Issue 552: BEAUTi keeps generating a dialog when load a binary datafile

6 lines of code changed in 1 file:

msuchard 2011-11-28 17:20 Rev.: 4496

Fixed typo in release properties and added BEAGLE operation reporter for infinite HMM work

627 lines of code changed in 4 files:

tbcbedford@gmail.com 2011-11-27 02:52 Rev.: 4495

Changed initial locations to aid convergence.

8 lines of code changed in 1 file:

dong.w.xie 2011-11-25 16:08 Rev.: 4494

trunk:solve Issue 515: cast Exception after click taxon set combo box in BEAUti Taxon Set panel

28 lines of code changed in 2 files:

dong.w.xie 2011-11-25 15:02 Rev.: 4493

trunk:solve Issue 551: remove rootHeight="?" from <coalescentTree> for MicroSat data

3 lines of code changed in 1 file:

dong.w.xie 2011-11-25 14:43 Rev.: 4492

trunk:solve Issue 550: MicroSat pattern does not generate properly

4 lines of code changed in 3 files:

dong.w.xie 2011-11-25 13:46 Rev.: 4491

trunk:solve Issue 549: BeautiOptions.updateAll() stop user to customize clock rates

44 lines of code changed in 6 files:

dong.w.xie 2011-11-25 11:16 Rev.: 4490

trunk:solve Issue 481: Improve reporting of XML errors

41 lines of code changed in 1 file:

rambaut 2011-11-25 03:50 Rev.: 4489

Added tip locations parameter to DATL

85 lines of code changed in 1 file:

philippe.lemey@gmail.com 2011-11-25 02:25 Rev.: 4488

Updating DnDsLoggerParser

6 lines of code changed in 1 file:

philippe.lemey@gmail.com 2011-11-25 00:38 Rev.: 4487

adding CnCsPerSiteAnalysis to parser list

2 lines of code changed in 1 file:

philippe.lemey@gmail.com 2011-11-25 00:35 Rev.: 4486

adding the possibility to log syn and nonsyn conditional/unconditional counts to DnDsLogger

102 lines of code changed in 1 file:

philippe.lemey@gmail.com 2011-11-25 00:28 Rev.: 4485

adding a trace analysis for syn and nonsyn counts

445 lines of code changed in 1 file:

rambaut 2011-11-24 21:41 Rev.: 4484

Merged my fix for error when ENABLE_ANCESTRAL_STATES = false.

14 lines of code changed in 1 file:

rambaut 2011-11-24 19:18 Rev.: 4483

Started to implement ancestral state reconstruction at a node.

99 lines of code changed in 10 files:

dong.w.xie 2011-11-24 14:30 Rev.: 4482

trunk:solve Issue 469: BEAUTi Covarion generation fails to add hfrequencies to operators.

2 lines of code changed in 1 file:

dong.w.xie 2011-11-24 11:00 Rev.: 4481

trunk:solve Issue 457: BEAST should raise an error if binary dataType set but data is not binary, and Issue 312: BEAST continues to run (inappropriately) when sequence contains invalid character

166 lines of code changed in 34 files:

msuchard 2011-11-24 01:57 Rev.: 4480

Moving parsers into release properties

321 lines of code changed in 4 files:

dong.w.xie 2011-11-23 14:22 Rev.: 4479

trunk:solve Issue 547: out of boundary if ENABLE_ANCESTRAL_STATES = false;

3 lines of code changed in 1 file:

dong.w.xie 2011-11-23 12:45 Rev.: 4476

trunk:solve Issue 546: disable link tree prior function in BEAUti if using EBSP and GMRF

15 lines of code changed in 4 files:

dong.w.xie 2011-11-23 10:49 Rev.: 4475

trunk:solve Issue 511: Multiple partitions not prefixing the names of 'patterns' correctly, but it may break AncestralStatesComponentGenerator and DolloComponentGenerator, and needs Andrew to review.

18 lines of code changed in 2 files:

julia.pal.r@gmail.com 2011-11-23 09:31 Rev.: 4474

Editing mainly GPSLikelihoodParser

137 lines of code changed in 4 files:

julia.pal.r@gmail.com 2011-11-22 19:21 Rev.: 4473

Creating evomodelxml..GaussianProcessSkytrackBlockUpdateOperator and renamed GPSkytrackBlockUpdateIperator from evomodel..

515 lines of code changed in 3 files:

julia.pal.r@gmail.com 2011-11-22 19:01 Rev.: 4472

Editing GaussianProcessSkytrackLikelihood.java and creating operators

466 lines of code changed in 2 files:

dong.w.xie 2011-11-22 16:33 Rev.: 4471

trunk:solve Issue 463: Correct BirthDeathSerialSampling xml generator in BEAUti because of parser changed

63 lines of code changed in 2 files:

dong.w.xie 2011-11-22 14:05 Rev.: 4470

trunk:solve Issue 452: Fixed rate relaxed molecular clock still generating upDownOperator on rate/ heights

21 lines of code changed in 3 files:

rambaut 2011-11-22 07:21 Rev.: 4469

Added explicit selection of dN/dS robust counting with additional citation text to keep Marc happy.

168 lines of code changed in 13 files:

tbcbedford@gmail.com 2011-11-22 02:04 Rev.: 4468

Fixed bug in calculation of log density in BiasedMultivariateDiffusionModel. Branches should properly scale with time now. This seems to be working.

9 lines of code changed in 4 files:

msuchard 2011-11-22 02:00 Rev.: 4467

Updated tool-text

14 lines of code changed in 1 file:

tbcbedford@gmail.com 2011-11-22 01:57 Rev.: 4466

Added statistic for specific virusLocations in analogy to what's present in DiscreteAntigenicLikelihood. Made a tweak to initial conditions to improve speed of convergence.

56 lines of code changed in 1 file:

rambaut 2011-11-22 00:02 Rev.: 4465

dNdS Robust counting now working?

25 lines of code changed in 1 file:

rambaut 2011-11-21 21:07 Rev.: 4464

Removed a few redundant imports

3 lines of code changed in 2 files:

rambaut 2011-11-21 12:11 Rev.: 4463

Deleting component 'dnds' as this is now handled by 'ancestralstates'

0 lines of code changed in 3 files:

rambaut 2011-11-21 11:58 Rev.: 4462

More work on generating ancestral state reconstruction

22 lines of code changed in 1 file:

rambaut 2011-11-21 11:48 Rev.: 4461

More work on generating ancestral state reconstruction

120 lines of code changed in 6 files:

rambaut 2011-11-21 03:37 Rev.: 4460

Starting to rebuild generation of robust counting.

26 lines of code changed in 3 files:

rambaut 2011-11-21 00:03 Rev.: 4459

Starting to rebuild generation of robust counting.

299 lines of code changed in 9 files:

rambaut 2011-11-20 22:00 Rev.: 4458

Added tool tips for all the tabs in BEAUti. The tabs are also now disabled until data is loaded to focus the user on what to do first.

55 lines of code changed in 2 files:

rambaut 2011-11-20 21:32 Rev.: 4457

Refactoring of the robust counting and sequence error model into a new tab ('States') which allows these options to be specified on a per partition basis. These options are still not finished yet but the panel can be hidden using the constant at the top of BeautiFrame.

294 lines of code changed in 3 files:

rambaut 2011-11-20 07:28 Rev.: 4456

Refactoring of the robust counting and sequence error model into a new tab ('States') which allows these options to be specified on a per partition basis. These options are still not finished yet but the panel can be hidden using the constant at the top of BeautiFrame.

880 lines of code changed in 42 files:

fbielejec 2011-11-19 23:15 Rev.: 4455

patched robust counting but it still needs testing

2 lines of code changed in 1 file:

julia.pal.r@gmail.com 2011-11-18 20:52 Rev.: 4454

Creating GaussianProcessSkytrackLikelihood.java

233 lines of code changed in 1 file:

rambaut 2011-11-18 19:20 Rev.: 4453

Added final exit(1) if BEAST itself throws an error

3 lines of code changed in 1 file:

dong.w.xie 2011-11-18 15:13 Rev.: 4452

trunk:solve Issue 465: BEAST v1.7pre has an exit status of 0 when exiting with an error

7 lines of code changed in 1 file:

dong.w.xie 2011-11-18 14:15 Rev.: 4451

trunk:solve Issue 493: Beauti does not show ploidy type for EBSP

1 lines of code changed in 1 file:

dong.w.xie 2011-11-18 10:22 Rev.: 4450

trunk: remove drop down list from TreePriorPanel, because the "none" functionality is provided
by the vanilla Yule. But still keep correctType in BEAUti options to make XML generate correctType = "exact".

13 lines of code changed in 1 file:

msuchard 2011-11-18 10:06 Rev.: 4449

Simple binary CTMCs can now parse using BEAGLE

86 lines of code changed in 2 files:

rambaut 2011-11-18 02:07 Rev.: 4448

Fixed a few issues with parsing string arrays.

9 lines of code changed in 7 files:

rambaut 2011-11-18 01:46 Rev.: 4447

Added ability to extract individual virus locations as statistics.

52 lines of code changed in 2 files:

dong.w.xie 2011-11-17 15:38 Rev.: 4446

trunk: solve Issue 545: BEAUti taxon set compatibility should be focused on each tree

2 lines of code changed in 1 file:

dong.w.xie 2011-11-17 14:56 Rev.: 4445

trunk: show Calibrated Yule in tree prior drop list

1 lines of code changed in 1 file:

dong.w.xie 2011-11-17 10:56 Rev.: 4444

trunk: Issue 543: BEAUti parameter getLowerBound() and getUpperBound() overwrite changes

2 lines of code changed in 1 file:

julia.pal.r@gmail.com 2011-11-17 10:44 Rev.: 4443

test

125 lines of code changed in 2 files:

dong.w.xie 2011-11-17 10:31 Rev.: 4442

trunk: fix a bug to use uniform lower and upper.

1 lines of code changed in 1 file:

rambaut 2011-11-17 09:49 Rev.: 4441

BeastGenerator's check function now throws GeneratorExceptions (rather than IllegalArgumentException). As a bonus this exception can specify the name of a Tab to switch to as an aid to the user to fix the issue.

72 lines of code changed in 3 files:

rambaut 2011-11-17 00:06 Rev.: 4440

Turned on SequenceErrorModel for BEAGLE

3 lines of code changed in 1 file:

rambaut 2011-11-16 21:59 Rev.: 4439

Fixed a few more '!' in user interface messages. Let's keep them for errors that shouldn't happen (i.e., are genuine surprises).

67 lines of code changed in 5 files:

rambaut 2011-11-16 21:52 Rev.: 4438

Removed '!' from warning and error messages as it kind of suggests the user is being dumb. Also adjusted the messages a bit for clarity.

6 lines of code changed in 1 file:

dong.w.xie 2011-11-16 16:46 Rev.: 4437

trunk: more on BEAUti calibrated Yule.

102 lines of code changed in 9 files:

dong.w.xie 2011-11-16 13:35 Rev.: 4436

trunk: update BEAUti calibrated Yule in *BEAST.

6 lines of code changed in 1 file:

rambaut 2011-11-16 05:15

Ported sequence error models to BeagleTreeLikelihood and implemented a variant model that emits tip states rather than tip partials.

420 lines of code changed in 27 files:

rambaut 2011-11-16 03:23 Rev.: 4432

Continuous trait generation now logs its branch rates with a different tag.

7 lines of code changed in 1 file:

rambaut 2011-11-16 03:18 Rev.: 4431

Added ability to log a specific tree trait using a different tag. XML looks like this (will log the second branch rates as 'trait.rate' whereas the first one will use its default 'rate'):

<logTree id="treeFileLog" logEvery="1000" nexusFormat="true" fileName="untitled.trees" sortTranslationTable="true">
<treeModel idref="treeModel"/>
<posterior idref="posterior"/>

<branchRates idref="branchRates"/>
<trait name="rate" tag="trait.rate">
<branchRates idref="trait.diffusionRates"/>
</trait>
</logTree>

31 lines of code changed in 1 file:

rambaut 2011-11-16 03:13 Rev.: 4430

Loggers weren't logging if they overrode the base class log(int state) - because it had been changed to log(long state). Put a final int version in the base class to prevent overriding.

66 lines of code changed in 25 files:

rambaut 2011-11-16 00:45 Rev.: 4429

Made BranchRateModel a TreeTraitProvider so it can be logged more easily. Also added feature to TreeLoggerParser where a tree trait can be specified (with a special tag).

66 lines of code changed in 9 files:

msuchard 2011-11-16 00:36 Rev.: 4428

Helping FLU model parsing.

28 lines of code changed in 1 file:

rambaut 2011-11-16 00:16 Rev.: 4427

Added FLU aa model to parser (and put a check for unknown model names).

4 lines of code changed in 1 file:

dong.w.xie 2011-11-15 16:33 Rev.: 4426

trunk: finish calibrated Yule, but may have bugs.

202 lines of code changed in 11 files:

rambaut 2011-11-15 09:42 Rev.: 4425

Missing DBRM from MTL in generated XML.

8 lines of code changed in 1 file:

rambaut 2011-11-15 09:26 Rev.: 4424

Upgraded chain length to a 64 bit integer so that chain lengths > 2.1 billion can be done. This addresses issue 540. Runs OK, accepts long chain lengths but not actually tested a run of > 2.1 billion.

108 lines of code changed in 25 files:

rambaut 2011-11-15 05:14 Rev.: 4423

Added citations to amino acid models and a text box in BEAUti.

208 lines of code changed in 21 files:

rambaut 2011-11-15 03:23 Rev.: 4422

When creating partitions from traits, doesn't allow mixed trait types and creates individual partitions for discrete traits but a single multivariate partition for continuous traits.

37 lines of code changed in 3 files:

rambaut 2011-11-15 01:29 Rev.: 4421

Switched BEAGLE to use scaling=always by default (i.e., if no command line option is specified). This will help prevent issues with large datasets (and won't slow small ones down much). Use "-beagle_scaling dynamic" to get the previous scaling behaviour.

2 lines of code changed in 2 files:

rambaut 2011-11-15 01:28 Rev.: 4420

Fixed issue with generation of replicate substitution models when multiple discrete traits are used

6 lines of code changed in 1 file:

rambaut 2011-11-15 01:03 Rev.: 4419

Fixed initial parameter settings for continuous trait gammaRRW gamma distribution.

1 lines of code changed in 1 file:

rambaut 2011-11-15 00:50 Rev.: 4418

Fixed a few issues with BSSVS generation. Also robust counting. Also unified the RECONSTRUCTION_TAG_NAME for the BEAGLE and non-BEAGLE versions of ASTL.

27 lines of code changed in 5 files:

rambaut 2011-11-14 22:36 Rev.: 4417

Improvement on fix for Issue 539 - making the text area non-opaque lets the background come through. This improves the Mac look as it is in a recessed box (a darker shade that the window background). I guess this looks OK on other platforms too?

2 lines of code changed in 1 file:

dong.w.xie 2011-11-14 16:34 Rev.: 4416

trunk: solve Issue 538: move tree prior panel to the left of table, and Issue 539: use the same background in citation text area in Tree panel, and some more code for calibrated Yule

160 lines of code changed in 8 files:

rambaut 2011-11-11 23:58 Rev.: 4415

DiscreteTraitBranchRateModel with Markov rewards

58 lines of code changed in 4 files:

rambaut 2011-11-11 23:58 Rev.: 4414

Added node-density feature to Pathogen

77 lines of code changed in 2 files:

rambaut 2011-11-11 23:48

Reorganization of the examples/release folder. Please add/remove anything that will be packaged with the next release.

2540 lines of code changed in 11 files:

rambaut 2011-11-11 23:37

Reorganization of the examples/release folder. Please add/remove anything that will be packaged with the next release.

0 lines of code changed in 18 files:

rambaut 2011-11-11 23:32

Reorganization of the examples/release folder. Please add/remove anything that will be packaged with the next release.

20501 lines of code changed in 80 files:

rambaut 2011-11-11 22:06 Rev.: 4404

Fixes for continuous trait generation.

13 lines of code changed in 1 file:

rambaut 2011-11-10 21:50

Only uses ancestralTreeLikelihood if robustCounting is selected for a particular partition model.

11 lines of code changed in 4 files:

dong.w.xie 2011-11-09 11:59 Rev.: 4401

improve enum CorrectionType to suit for BEAUti, and finish Calibrated Yule GUI part, but need further work on xml generator.

181 lines of code changed in 6 files:

dong.w.xie 2011-11-09 11:32 Rev.: 4400

solve Issue 485: BEAUti trunk: tree prior is locked at Coalescent Constant, and Issue 536: Species tree prior is locked, and more dev on Calibrated Yule in BEAUti

17 lines of code changed in 5 files:

dong.w.xie 2011-11-09 10:46 Rev.: 4399

solve Issue 535: SpeciesTreesPanel are not necessary

149 lines of code changed in 4 files:

dong.w.xie 2011-11-08 16:55 Rev.: 4398

trunk: start BEAUti dev Calibrated Yule

9 lines of code changed in 3 files:

dong.w.xie 2011-11-08 11:12 Rev.: 4397

trunk: solve Issue 534: *BEAST needs validate species set

24 lines of code changed in 1 file:

dong.w.xie 2011-11-08 10:55 Rev.: 4396

trunk: solve Issue 533: Taxon set validation fires twice

2 lines of code changed in 3 files:

tbcbedford@gmail.com 2011-11-08 06:09 Rev.: 4395

Reverting change to mapping of viruses to sera. Cannot be replicate rows in HI table.

2 lines of code changed in 1 file:

rambaut 2011-11-08 04:58 Rev.: 4394

Multiple virus aliases

6 lines of code changed in 1 file:

julia.pal.r@gmail.com 2011-11-07 18:07 Rev.: 4393

test

1 lines of code changed in 1 file:

rambaut 2011-11-07 03:43 Rev.: 4392

Cleaning up bugs in XML generation...

95 lines of code changed in 17 files:

rambaut 2011-11-06 02:48 Rev.: 4391

Oops. Messed up implementing logPDF for UniformDistribution.

1 lines of code changed in 2 files:

rambaut 2011-11-05 02:53 Rev.: 4390

More cleaning up and adjusting of uniform priors.

65 lines of code changed in 5 files:

vminin 2011-11-04 12:02 Rev.: 4389

How annoying can I get with these commits?

1 lines of code changed in 1 file:

vminin 2011-11-04 11:54 Rev.: 4388

Saving GP likelihood again

1 lines of code changed in 1 file:

vminin 2011-11-04 11:46 Rev.: 4387

Saving GP likelihood

1 lines of code changed in 1 file:

rambaut 2011-11-03 21:34 Rev.: 4386

Fixed issue 530: http://code.google.com/p/beast-mcmc/issues/detail?id=530. Now allows marginal prior on root height to be switched off.

42 lines of code changed in 1 file:

rambaut 2011-11-02 09:31 Rev.: 4385

More fixes for using uniform as a way of truncating distributions (should switch to using TruncatedDistribution to get correct normalization).

8 lines of code changed in 5 files:

rambaut 2011-11-01 21:59 Rev.: 4384

Trying to fix up the confusion with uniform bounds. The parameter object in beauti now has 'uniformUpper' and 'uniformLower' rather than using the truncationUpper/Lower (uniform prior cannot be truncated now). Changed the logPDF function of UniformDistribution to take the log before the reciprocal to reduce chance of underflow (note however that taking the log of Double.MAX_VALUE (or twice that if the lower bound is -MAX_VALUE) may still fail). Testing now being undertaken...

28 lines of code changed in 6 files:

rambaut 2011-11-01 19:47 Rev.: 4383

Reverted changes that made default uniform prior bounded at [-MAX_VALUE, MAX_VALUE]. The -Inf, Inf were being used to define an improper prior and to specify _no_ truncation on other distributions. If, when generating a uniform prior, there is an infinite bound, BEAUti now doesn't generate the prior at all but puts a comment that there is an improper uniform prior on the parameter.

15 lines of code changed in 2 files:

dong.w.xie 2011-11-01 14:21 Rev.: 4382

trunk: solve Issue 529: proper priors to determine calibration in BEAUti

10 lines of code changed in 1 file:

dong.w.xie 2011-11-01 14:03 Rev.: 4381

trunk: correct the bug created by previous fixes.

9 lines of code changed in 3 files:

dong.w.xie 2011-11-01 13:15 Rev.: 4380

trunk: solve Issue 527: change bound of Uniform prior into Double MAX or MIN, and Issue 528: the BEAST parser for UniformPrior should throw a parser exception if you attempt to give a bound at infinity.

10 lines of code changed in 2 files:

dong.w.xie 2011-11-01 13:00 Rev.: 4379

trunk: solve Issue 526: recover the function to allow different taxa in BEAUti

7 lines of code changed in 3 files:

dong.w.xie 2011-11-01 12:32 Rev.: 4378

trunk: solve Issue 525: BEAUti should link the trees for multi-partitions by default

1 lines of code changed in 1 file:

dong.w.xie 2011-11-01 11:25 Rev.: 4377

trunk: solve Issue 524: link/unlink tree prior not working properly in BEAUti

40 lines of code changed in 5 files:

rambaut 2011-11-01 05:07 Rev.: 4376

Additions to the comments.

4 lines of code changed in 1 file:

October 2011 »

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