April 2009 Commit Log

Number of Commits:
124
Number of Active Developers:
7
dong.w.xie 2009-04-30 17:42 Rev.: 1655

generate <species> and its sub-tags, but there is hard code in method writeTraits in BeastGeneratos, need to improve it to fit other traits.

79 lines of code changed in 3 files:

dong.w.xie 2009-04-30 13:53 Rev.: 1654

Add boolean containsAttribute(String name) to check whether Taxon contains the attribute by given its name, if attributes == null, return false.

20 lines of code changed in 2 files:

jheled 2009-04-30 13:27 Rev.: 1653

Load traits from a file for beauti. File is tab delimeted.
The first line contains the lables, including the first column.
If the first column is a trait name, it is followed by the trait value and a list of taxa.

132 lines of code changed in 2 files:

msuchard 2009-04-30 10:00 Rev.: 1652

Merged SpatialTemporalPolygon and Polygon2D (both function now at the same fast speed); will remove STP once all references changed

109 lines of code changed in 1 file:

msuchard 2009-04-30 08:28 Rev.: 1651

LoggableStatistic turns a Loggable into a Statistic; minor tweaks in Polygon2D (still not sure why contains() takes 3 times longer than in the old Polygon class.

194 lines of code changed in 7 files:

dong.w.xie 2009-04-29 16:50 Rev.: 1650

Add parser in Utils and change importTraitsFromFile to distinguish Joseph and Andrew's trait file format (not finished yet).

99 lines of code changed in 2 files:

dong.w.xie 2009-04-29 13:53 Rev.: 1649

Make build work for dr.java16compat.*

3 lines of code changed in 1 file:

jheled 2009-04-29 10:47 Rev.: 1648

add more common extensions

1 lines of code changed in 1 file:

jheled 2009-04-29 10:00 Rev.: 1647

Sorry - set the package name correctly

8 lines of code changed in 4 files:

jheled 2009-04-29 09:41 Rev.: 1646

Add filter to select only .log files

10 lines of code changed in 1 file:

jheled 2009-04-29 09:32 Rev.: 1645

Java 1.6 backwards compatibility for file chooser

183 lines of code changed in 2 files:

jheled 2009-04-29 09:03 Rev.: 1644

Don't throw an exception if no taxa loaded yet

33 lines of code changed in 1 file:

dong.w.xie 2009-04-28 17:10 Rev.: 1643

Add new taxon in taxonList for the rest genes, if different taxon names allowed in multi-files.
Make Beauti to import multi Nex & Beast files at one time, and add file filter and remember the previous path.

66 lines of code changed in 1 file:

dong.w.xie 2009-04-27 16:31 Rev.: 1642

Remove List<TaxonList> multiTaxaList, previously used for creating unique taxon name combining gene's name in taxa tag for multi-taxa case.

16 lines of code changed in 3 files:

msuchard 2009-04-27 15:12 Rev.: 1641

Hierarchical Gibbs operators work.

146 lines of code changed in 6 files:

msuchard 2009-04-27 13:53 Rev.: 1640

Working on hierarchical models

395 lines of code changed in 9 files:

rambaut 2009-04-26 09:48 Rev.: 1639

Extended linking/unlinking to include trees by mirroring the setup we use for substitution models. Not complete yet so have included a static switch in DataPanel.ALLOW_UNLINKED_TREES which when false, reverts to the old GUI.

1313 lines of code changed in 20 files:

rambaut 2009-04-26 06:46 Rev.: 1638

Made some improvements to TaxonList and Taxa to make them work better with collections. For a start TaxonList is now Iterable so can be used in a for(Taxon taxon : taxonList) construct. In the long run we would be better dropping TaxonList and just replacing it with List<Taxon>.

453 lines of code changed in 22 files:

rambaut 2009-04-26 05:52 Rev.: 1637

Made some improvements to TaxonList and Taxa to make them work better with collections. For a start TaxonList is now Iterable so can be used in a for(Taxon taxon : taxonList) construct. In the long run we would be better dropping TaxonList and just replacing it with List<Taxon>.

106 lines of code changed in 3 files:

rambaut 2009-04-26 03:39 Rev.: 1636

Data panel now allows linking/unlinking of trees. These trees will be set/edited etc in the TreesPanel which will become the analogue of ModelPanel.

951 lines of code changed in 13 files:

rambaut 2009-04-26 02:03 Rev.: 1635

Traits panel now imports traits (from both a button in the panel and "Import Traits" in the File menu). You can select and view traits for taxa. You can create new traits (but not edit the trait values for taxa yet). There is still quite a lot of 'user error behaviour' to add. I have been a bit brutal and deleted the loading of 'Species Maps' from the Data Panel as this was too specific, in the wrong place and duplicated the trait loading stuff.

805 lines of code changed in 4 files:

rambaut 2009-04-25 22:12 Rev.: 1634

Continued development of the Traits panel

770 lines of code changed in 9 files:

jheled 2009-04-25 18:20 Rev.: 1633

apparently a bug - exception not thrown

1 lines of code changed in 2 files:

jheled 2009-04-25 18:16 Rev.: 1632

Change comment in readFileIntoMap to reflect the generic nature of the function. clean up code a little.

37 lines of code changed in 1 file:

alexei.drummond 2009-04-24 23:41 Rev.: 1631

added a few simple log normal distribution tests. All distributions should have some simple tests like this.

151 lines of code changed in 2 files:

dong.w.xie 2009-04-24 17:01 Rev.: 1630

More work on Multispecies Coalescent for BEAUTI, try to implement mapping between species and taxa.

129 lines of code changed in 6 files:

jheled 2009-04-24 12:36 Rev.: 1629

Inverse gamma distribution

392 lines of code changed in 6 files:

jheled 2009-04-24 10:39 Rev.: 1628

A generic scale operator similar to the one used in MrBayes. Operates like a random walk with a fixed window size in log space. Thanks for David Bryant for figuring out the hastings ratios.

220 lines of code changed in 2 files:

msuchard 2009-04-24 08:05 Rev.: 1627

Refactored RateEpochBranchRateModel to remove repeated code in ContinuousEpochBranchRateModel

17 lines of code changed in 2 files:

msuchard 2009-04-24 06:51 Rev.: 1626

Fixed bug in LogNormalDistributionModel parser (was not constructing a distribution with a precision)

1 lines of code changed in 1 file:

rambaut 2009-04-24 01:42 Rev.: 1625

Created a 'CompoundBranchRateModel' which takes 2 or more BranchModels and returns the product of their rates for the respective branches. Have tested it by combining a RateEpochModel with a DiscretizedBranchRateModel and it seems to work fine. You need to take care to make one model give relative rates and the other absolute (i.e., avoid over-parameterization).

147 lines of code changed in 2 files:

dong.w.xie 2009-04-23 17:12 Rev.: 1624

More work on Multispecies Coalescent for BEAUTI

108 lines of code changed in 4 files:

rambaut 2009-04-23 10:43 Rev.: 1623

A few small changes for trait loading/displaying.

41 lines of code changed in 3 files:

rambaut 2009-04-23 10:27 Rev.: 1622

Added a menu command to annotate taxa with traits read from a file.

44 lines of code changed in 4 files:

dong.w.xie 2009-04-23 10:15 Rev.: 1621

It currently is a copy of TipDatesPanel, and will be implemnted late.

0 lines of code changed in 1 file:

dong.w.xie 2009-04-23 09:47 Rev.: 1620

The initial change to implement Multispecies coalescent user inference in BEAUTI

63 lines of code changed in 2 files:

rambaut 2009-04-22 19:27 Rev.: 1619

Fixing issue 81 - it was an erroneous import of a class from without BEAST.

13 lines of code changed in 1 file:

msuchard 2009-04-22 11:14 Rev.: 1618

For consistency with NormalDistributionModel, 'prec' in parsers changed to 'precision'

1 lines of code changed in 1 file:

msuchard 2009-04-22 10:40 Rev.: 1617

ARGModel now fully supports caching partial likelihood calculations even as nodes are added and remove from tree. Support is not fully implemented in the operators yet.

228 lines of code changed in 11 files:

rambaut 2009-04-22 09:36 Rev.: 1616

Further work on BEAUti. Added options to allow sampling of tip dates.

1151 lines of code changed in 15 files:

rambaut 2009-04-22 00:24 Rev.: 1615

Lots of work on BEAUti

Started work on a modularization of BEAST generation (look in beauti.components). Lots of insertion points are defined throughout the BEAST file (relative to all the standard content) and a component can offer to write content to each or any of these. Instances of each component are created in BeautiFrame constructor. Started converting some of the monolithic generation into components (see SequenceErrorModel for an example).

Implemented the ability to import an existing BEAST file but at the moment the taxa, dates and sequences are all that are picked up.

Started work on a 'locations' tab but am currently uncertain whether this shouldn't just be a general traits tab.

Save/Apply templates menu options are hidden as we don't have an implementation yet.

1836 lines of code changed in 26 files:

dong.w.xie 2009-04-21 15:02 Rev.: 1614

Synchronize to build_release.xml by adding dr/geo

3 lines of code changed in 1 file:

dong.w.xie 2009-04-21 12:44 Rev.: 1613

Modify ant to give framed JUnit test report.

2 lines of code changed in 1 file:

msuchard 2009-04-21 11:40 Rev.: 1612

Messing around with epoch models for continuous diffusion

5 lines of code changed in 2 files:

dong.w.xie 2009-04-20 14:32 Rev.: 1611

Modify build_BEAST_MCMC to include more JUnit test.

9 lines of code changed in 1 file:

dong.w.xie 2009-04-20 14:30 Rev.: 1610

Wrong location of this class, move it from test.dr.inference.distribution into dr.inference.distribution.

0 lines of code changed in 2 files:

msuchard 2009-04-20 14:21 Rev.: 1609

Modified MultivariateTraitLikelihood to ouput the sampling density of observed data alone

44 lines of code changed in 2 files:

msuchard 2009-04-20 12:48 Rev.: 1608

Started overhaul of ARG model likelihood calculations to cache unaffected partials (it's about time I did this). All changes to the ARG model, except for topological changes, appear to be caching correctly; speed-up is about 30% (for a small example, suspect much more for larger problems). I need to think harder about how to handle topological changes -- a simple map from old ARGTree nodes to ARGModel to new ARGTree nodes should suffice.

196 lines of code changed in 6 files:

jheled 2009-04-20 09:10 Rev.: 1607

Continued Marc's refactorization. I wonder what other shared functionality we can pull off in there.

12 lines of code changed in 18 files:

jheled 2009-04-20 09:10 Rev.: 1606

Check evaluation after accept move as well. chaeck until at least N (=1) accpets and rejects for each operator.

27 lines of code changed in 4 files:

msuchard 2009-04-20 06:05 Rev.: 1605

Refactored LikelihoodColumn as protected class in AbstractModelLikelihood (thanks, Joseph ... this was a good idea); removed subclassing of getLogColumns in several AMLs to see if this break things. I do not suspect that it will and we can/should now remove subclassing getLogColumns and redefinition of LikelihoodColumn in most AMLs, saving hundreds of lines of code .. or shotting myself in the foot :-)

728 lines of code changed in 14 files:

msuchard 2009-04-20 03:18 Rev.: 1604

Forgot to add months ago

1 lines of code changed in 1 file:

msuchard 2009-04-19 13:23 Rev.: 1603

MultivariateTraitLikelihood now supports (not default) caching of branch-likelihoods; however, caching has a slightly slower run-time for simple 2D Brownian diffusion. Normalizing by treeLengths means that all tree changes result in a complete recalculation anyway. Advantages may be seen as diffusion models get more complicated or with treeHeight normalization

331 lines of code changed in 2 files:

msuchard 2009-04-19 10:01 Rev.: 1602

Includes dr/geo directories

4 lines of code changed in 1 file:

msuchard 2009-04-19 09:49 Rev.: 1601

Including a non-map reproduces 2D Brownian for comparison and testing

18 lines of code changed in 2 files:

jheled 2009-04-19 08:39 Rev.: 1600

automatic intelliJ inspection

30 lines of code changed in 6 files:

jheled 2009-04-19 08:36 Rev.: 1599

comments and cosmetic

27 lines of code changed in 3 files:

jheled 2009-04-19 08:35 Rev.: 1598

add a nethod for getting a meaningfull name of a likelihood. more classes may benefit from overriding the default.

253 lines of code changed in 40 files:

jheled 2009-04-19 08:21 Rev.: 1597

use exchangeNodes explicitly. remove historical eupdate

4 lines of code changed in 1 file:

jheled 2009-04-19 08:17 Rev.: 1596

comment out unused code

267 lines of code changed in 1 file:

rambaut 2009-04-18 22:06 Rev.: 1595

Slight modification of when the fullEvaluation test is performed.

1 lines of code changed in 1 file:

jheled 2009-04-18 16:57 Rev.: 1594

First lame attempt fo fix issue 78

44 lines of code changed in 1 file:

jheled 2009-04-18 16:12 Rev.: 1593

Temporary fix for issue 79.

6 lines of code changed in 1 file:

msuchard 2009-04-18 06:23 Rev.: 1592

CartogramDiffusionModel runs; am still unsure on normalization of 2D diffusion approximation for GreatCircleDiffusionModel and CartogramDiffusionModel

39 lines of code changed in 5 files:

dong.w.xie 2009-04-17 14:52 Rev.: 1591

Modify build_BEAST_MCMC to include more JUnit test

3 lines of code changed in 1 file:

dong.w.xie 2009-04-17 14:48 Rev.: 1590

Correct more JUnit test.

209 lines of code changed in 13 files:

msuchard 2009-04-17 12:25 Rev.: 1589

Cleaning up precision Gibbs operator in the hope that it works

42 lines of code changed in 2 files:

msuchard 2009-04-17 11:38 Rev.: 1588

Yet another bug fix in MultivariateNormalDistribution

29 lines of code changed in 4 files:

Sebastian.Hoehna 2009-04-16 23:27 Rev.: 1587

More stuff from my Masters project ...

845 lines of code changed in 4 files:

Sebastian.Hoehna 2009-04-16 23:26 Rev.: 1586

Some more stuff on the tree proposal operators. Commiting sources from Masters project and some clean ups.

Remark: CCPImportanceDistributionOperator is working, but not efficient. Further work needs to be done.

1144 lines of code changed in 4 files:

dong.w.xie 2009-04-16 16:54 Rev.: 1585

Correct JUnit Test to make BEAST complied successfully.

4 lines of code changed in 1 file:

dong.w.xie 2009-04-16 13:19 Rev.: 1584

Modify ANT build_BEAST_MCMC.xml to include JUnit test.

54 lines of code changed in 1 file:

dong.w.xie 2009-04-16 13:16 Rev.: 1583

Correct the committed JUnit test files and make them working.

36 lines of code changed in 4 files:

msuchard 2009-04-16 08:26 Rev.: 1582

Repaired bug in MultivariateNormalDistribution

36 lines of code changed in 2 files:

msuchard 2009-04-15 16:13 Rev.: 1581

BEAGLE-java now supports dynamic under/over-flow rescaling

0 lines of code changed in 1 file:

dong.w.xie 2009-04-15 14:46 Rev.: 1580

Create ANT to make individual jar for tools in BEAST.

0 lines of code changed in 1 file:

dong.w.xie 2009-04-15 14:45 Rev.: 1579

Create ANT to build BEAST_MCMC including BEAUTI.

179 lines of code changed in 1 file:

dong.w.xie 2009-04-15 14:44 Rev.: 1578

rename bin into scripts. Always add scripts into scripts folder. bin will be used only for build.

0 lines of code changed in 10 files:

dong.w.xie 2009-04-15 14:39 Rev.: 1577

Always add scripts into scripts folder. bin will be used only for build.

0 lines of code changed in 1 file:

dong.w.xie 2009-04-15 14:34 Rev.: 1576

add beagle.jar, figtreepanel.jar and jam.jar into lib path.

12 lines of code changed in 1 file:

dong.w.xie 2009-04-15 14:03 Rev.: 1575

Correct the existing JUnit test.

45 lines of code changed in 10 files:

msuchard 2009-04-15 12:17 Rev.: 1574

Fixed up the monotonic statistic for constraining parameters and what-not.

120 lines of code changed in 3 files:

Sebastian.Hoehna 2009-04-15 01:05 Rev.: 1573

Tidying up to resolve more the confusion between the Gibbs and Metropolized Gibbs Proposals.

3 lines of code changed in 2 files:

Sebastian.Hoehna 2009-04-14 23:42 Rev.: 1572

Change name of SimpleGibbsOperator to SimpleMetropolizedGibbsOperator to avoid confusion.

167 lines of code changed in 5 files:

msuchard 2009-04-14 12:06 Rev.: 1571

Debugging hidden codon models and need to test on larger computer system.

181 lines of code changed in 8 files:

rambaut 2009-04-14 09:53 Rev.: 1570

Full evaluation continues until every operator has done at least one operation. If an error has occurred in this time, then a runtime exception is thrown.

32 lines of code changed in 1 file:

rambaut 2009-04-14 09:01 Rev.: 1569

Added a getCount to the operator interface and a getMinimumCount to OperatorSchedule. This gives the number of times the least frequently used operator has been called.

420 lines of code changed in 14 files:

rambaut 2009-04-14 06:44 Rev.: 1568

Broke the build with my last clean up (removing a hack in MarkovChain). Sorry.

12 lines of code changed in 4 files:

msuchard 2009-04-13 12:21 Rev.: 1567

Rescaling by tree length in MultivariateTraitLikelihood appears to solve normalization issue

24 lines of code changed in 1 file:

rambaut 2009-04-13 11:09 Rev.: 1566

Cleaned up MarkovChain a little more. There were some debug printfs surrounded by if statements. Made the flag that turned these on into a static final - this should mean the if statements will not be compiled in if false.

Added comment about odd coding surrounding Gibbs operators - don't want to fiddle but looks suspect to me.

16 lines of code changed in 1 file:

jheled 2009-04-13 08:18 Rev.: 1565

java 1.5 features

1 lines of code changed in 1 file:

jheled 2009-04-13 08:17 Rev.: 1564

Implement scaling only one element via scalable interface.

130 lines of code changed in 4 files:

jheled 2009-04-13 08:14 Rev.: 1563

Fix problem uncoverd by Andrew's new test

34 lines of code changed in 1 file:

jheled 2009-04-13 08:13 Rev.: 1562

Two new operators

528 lines of code changed in 2 files:

jheled 2009-04-13 07:56 Rev.: 1561

code police

811 lines of code changed in 15 files:

jheled 2009-04-13 07:53 Rev.: 1560

Better names for sub-statistic elements

18 lines of code changed in 1 file:

rambaut 2009-04-12 23:24 Rev.: 1559

Commented out two calls to pushTreeChangedEvent() in narrow exchange. No other exchange operation has these and removing them did not cause the new test in MarkovChain to fail (removing the same event in tree.addChild() did fail this test).

2 lines of code changed in 1 file:

rambaut 2009-04-12 23:21 Rev.: 1558

Added an additional test of full evaluation of the likelihood after an operator. This should detect operators that don't fully flag up what to update.

I also removed a likelihood.makeDirty() call that was removing efficiency savings on restore. This was presumably a work around for a bug in another class. We should expect the test of full evaluation after restore test to fail on some models (but who knows what? This call was masking the test of correct restore). Benchmark.xml works with this call removed.

25 lines of code changed in 1 file:

jheled 2009-04-11 09:40 Rev.: 1557

The "pattern of site" mapping is broken. I appriciate it if someone more familiar with this code audit my fix.

16 lines of code changed in 2 files:

rambaut 2009-04-10 20:10 Rev.: 1556

Added a statistic to TreeLikelihoods to get the likelihoods for each site.

34 lines of code changed in 1 file:

rambaut 2009-04-10 11:03 Rev.: 1555

Added indicator statistic labelled with sequence name

31 lines of code changed in 3 files:

rambaut 2009-04-10 10:40 Rev.: 1554

APOBEC model clean up

8 lines of code changed in 1 file:

rambaut 2009-04-10 03:13 Rev.: 1553

Another fix to UniformRootPrior

7 lines of code changed in 1 file:

rambaut 2009-04-10 02:54 Rev.: 1552

Fixed density for UniformRootPrior with dated tips

52 lines of code changed in 1 file:

alexei.drummond 2009-04-09 15:58 Rev.: 1551

removed confusing incorrect comments

0 lines of code changed in 1 file:

jheled 2009-04-09 14:43 Rev.: 1550

automatic idea changes

528 lines of code changed in 14 files:

jheled 2009-04-09 14:42 Rev.: 1549

cosmetic

271 lines of code changed in 2 files:

jheled 2009-04-09 13:30 Rev.: 1548

Give model a more useful name

2 lines of code changed in 1 file:

jheled 2009-04-09 13:29 Rev.: 1547

Make starting size optional - compute srating size from tree if necessary

18 lines of code changed in 1 file:

jheled 2009-04-09 13:26 Rev.: 1546

Add convenience uniform method

16 lines of code changed in 1 file:

rambaut 2009-04-08 11:19 Rev.: 1542

Forgot to check in changes to Coevolve. What is Coevolve? Looks like old crud that should be deleted.

10 lines of code changed in 1 file:

alexander.alekseyenko 2009-04-08 09:36 Rev.: 1541

minor adjustments to path sampling code
1) user can specify the amount of burn-in through a corresponding attribute
2) the pathParameter column is now labeled as such; this was done by fixing how properties get logged

172 lines of code changed in 6 files:

rambaut 2009-04-08 04:35 Rev.: 1540

Added Location to core parsers

1 lines of code changed in 1 file:

rambaut 2009-04-08 04:33 Rev.: 1539

Made it easier to set up CTMC of locations by allowing GeneralDataTypeParser to take Identifyable objects as states (such as a set of Location objects). The AttributePatternsParser can then extract the states from attributes of the taxa.

352 lines of code changed in 10 files:

rambaut 2009-04-08 04:20 Rev.: 1538

Added a demo Beagle core that uses the dependencies of node operations to add additional parallelization. Probably not worth doing in Java but maybe worth porting to CUDA.

46 lines of code changed in 1 file:

msuchard 2009-04-07 22:17 Rev.: 1537

Attempting treeHeight scaling in MultivariateTraitLikelihood (again)

6 lines of code changed in 1 file:

msuchard 2009-04-07 21:19 Rev.: 1536

Added DuplicatedParameter for symmetric rates and assymetric indicators. Added ColtEigenSystem to compare numerical stability in beagle package.

251 lines of code changed in 10 files:

msuchard 2009-04-07 02:24 Rev.: 1535

Reorder internal representation of complex rates; added a rate exchange operator for philippe.

115 lines of code changed in 3 files:

msuchard 2009-04-06 10:56 Rev.: 1534

Working on path sampling final integration code; some fixes in CompoundSymmetricMatrix to enable MH proposals and retain positive definiteness.

141 lines of code changed in 8 files:

msuchard 2009-04-02 12:08 Rev.: 1533

Started parser to compute bayes factor from path sampling chain.

166 lines of code changed in 1 file:

rambaut 2009-04-01 11:52 Rev.: 1532

Fixed problem with ambiguous states. Removed unneccesary allocation of partials/states.

18 lines of code changed in 1 file:

jheled 2009-04-01 10:27 Rev.: 1531

Make species tree scalable.

42 lines of code changed in 2 files:

jheled 2009-04-01 10:26 Rev.: 1530

Generalize up down operator - Allow any object which supports the "Scalable" interface. Allow any number of scalables in the up/down section. Provide backward compatability for parameters.

305 lines of code changed in 2 files:

msuchard 2009-04-01 08:32 Rev.: 1529

Apache Poisson PDF returns NaN if fails; bug fixed in how BEAST handles this case.

1 lines of code changed in 2 files:

March 2009 »

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