March 2009 Commit Log

Number of Commits:
65
Number of Active Developers:
6
msuchard 2009-03-31 12:18 Rev.: 1528

Removed NativeSubstitutionModel (old, defunct code for GPU) and started working on a covarion-like codon models. Here come the 128 and 196 state models!

184 lines of code changed in 4 files:

rambaut 2009-03-31 02:23 Rev.: 1527

An experimental model for detecting and accommodating hypermutation in HIV-1 caused by APOBEC 3G or 3F.

3 lines of code changed in 1 file:

rambaut 2009-03-31 02:17 Rev.: 1526

APOBEC model...

17 lines of code changed in 1 file:

rambaut 2009-03-31 01:42 Rev.: 1525

fixed typo in ReciprocalRateDistributionModel

1 lines of code changed in 2 files:

rambaut 2009-03-31 01:40 Rev.: 1524

An experimental model for detecting and accommodating hypermutation in HIV-1 caused by APOBEC 3G or 3F.

16 lines of code changed in 1 file:

Sibon.Li@gmail.com 2009-03-30 16:59 Rev.: 1523

Added class for the 1/rate model. Currently in a test folder

6 lines of code changed in 1 file:

Sibon.Li@gmail.com 2009-03-30 16:31 Rev.: 1522

Added class for the 1/rate model. Currently in a test folder

344 lines of code changed in 1 file:

rambaut 2009-03-28 10:25 Rev.: 1521

An experimental model for detecting and accommodating hypermutation in HIV-1 caused by APOBEC 3G or 3F.

199 lines of code changed in 1 file:

msuchard 2009-03-28 09:18 Rev.: 1520

BeagleTreeLikelihood and the BEAGLE library now support the dynamic partials rescaling that we have come to know and love.

3 lines of code changed in 4 files:

msuchard 2009-03-27 10:46 Rev.: 1519

TreeAnnotator can now spit out the ancestral state spectrum, in addition to the modal state.

19 lines of code changed in 1 file:

jheled 2009-03-27 09:51 Rev.: 1518

ongoing sp tree development

536 lines of code changed in 7 files:

jheled 2009-03-27 09:49 Rev.: 1517

automatic idea changes

34 lines of code changed in 10 files:

jheled 2009-03-27 09:44 Rev.: 1516

Add option for a tree logger to log states based upon an external condition

25 lines of code changed in 2 files:

msuchard 2009-03-25 07:34 Rev.: 1515

Changed BEAGLE tree parser so user can specify a precision preference instead of requirement. Removed some redundant code (static names)

16 lines of code changed in 4 files:

rambaut 2009-03-25 06:23 Rev.: 1514

Goldman Yang 94 model ported to beagle

491 lines of code changed in 3 files:

rambaut 2009-03-25 04:40 Rev.: 1513

Added an alternative parameterization of PiecewiseExponential that has a vector of pop sizes and a final ancestral growth rate. This should help with mixing (having a vector of growth rates was problematic because of the interaction between adjacent rates).

194 lines of code changed in 4 files:

msuchard 2009-03-25 02:03 Rev.: 1512

The CUDA version of BEAGLE requires that each getLogLikelihood() be called from the same thread each time (known incompatibility); CompoundLikelihood uses a pool, while ThreadedCompoundLikelihood has static allocation. Fixed missing files in build_development.xml

7 lines of code changed in 3 files:

rambaut 2009-03-24 23:20 Rev.: 1511

Created a BEAGLE specific parser for <likelihood> that puts child TreeLikelihoods into threads.

78 lines of code changed in 2 files:

rambaut 2009-03-24 05:11 Rev.: 1510

Import optimization

8 lines of code changed in 1 file:

rambaut 2009-03-24 05:09 Rev.: 1509

Cleaned up the test folder.

0 lines of code changed in 1 file:

rambaut 2009-03-22 11:37 Rev.: 1508

BEAGLE (CPU version) seems to be working.

0 lines of code changed in 1 file:

jheled 2009-03-22 09:16 Rev.: 1507

spelling

1 lines of code changed in 1 file:

rambaut 2009-03-21 23:08 Rev.: 1506

Improved interface of calculateTransitionProbabilityMatrices to allow multiple branches to be updated. Eliminated use of getCriticalPrimativeArray over calls to BEAGLE. Elimated mallocs within JNIWrapper calls. However, the native CPU version seems not to work yet (zero likelihood).

1 lines of code changed in 1 file:

rambaut 2009-03-21 09:52 Rev.: 1505

2 lines of code changed in 1 file:

rambaut 2009-03-20 05:08 Rev.: 1504

Towards a working beagle library

342 lines of code changed in 9 files:

msuchard 2009-03-19 09:17 Rev.: 1503

Performs simple spatial operators [Polygon.contains(Point) and Polygon.clip(Rectangle)] for Philippe

246 lines of code changed in 1 file:

rambaut 2009-03-19 05:23 Rev.: 1502

Towards a working beagle library

95 lines of code changed in 8 files:

rambaut 2009-03-19 02:15 Rev.: 1501

I have moved all the new stuff for the 'BEAGLE' library into its own package. I am producing a set of parsers that override the default ones to use the new classes. I envisage that at some point we will want to move to the new SubstModel hierarchy as it is much cleaner. But to avoid breaking anything whilst this develops, I am compartmentalizing them.

3505 lines of code changed in 39 files:

rambaut 2009-03-18 23:48 Rev.: 1500

More BEAGLE tweaks (BEAGLE is the name we (Marc & Andrew) have given to the cross-platform, cross-application, CTMC likelihood evaluation library. The idea is that it produces a fast, abstract API that can be used by many programs and which can have GPU implementations (CUDA, OpenCL) as well as just fast native ones.

236 lines of code changed in 3 files:

rambaut 2009-03-18 20:16 Rev.: 1499

Sorry for the broken build. Add the new library 'lib/beagle.jar' to your project.

0 lines of code changed in 1 file:

rambaut 2009-03-18 10:40 Rev.: 1498

Integrated BEAGLE into BEAST (compiles and runs but crashes in native code).

663 lines of code changed in 10 files:

msuchard 2009-03-18 07:46 Rev.: 1497

Add ability to import results from Mark Newan's 'cartogram' program and use the density equalized map as a diffusion transformation

282 lines of code changed in 2 files:

msuchard 2009-03-16 11:26 Rev.: 1496

Added analytic eigendecomposition of HKY model for BEAGLE likelihood evaluator

112 lines of code changed in 6 files:

rambaut 2009-03-14 22:49 Rev.: 1495

Made a few changes about how parsers are dealt with. The BeastParser class can now be given a list of additional parser lists to attempt to load. For example the command line option '-vector' now adds the parser list vector_parsers.properties to the mix. In addition, parsers in the additional lists can override previously loaded ones. In vector_parsers.properties is a parser called dr.evomodel.newtreelikelihood.TreeLikelihood that overrides the default TreeLikelihood with the new one that can use the GPU. This means we can switch on GPU using the -vector command line.

102 lines of code changed in 10 files:

msuchard 2009-03-12 13:26 Rev.: 1494

Irreversible BSSVS models now optionally check to be strongly (directionally) connected. Enabled condition number checking and believe it works.

26 lines of code changed in 2 files:

msuchard 2009-03-12 11:23 Rev.: 1493

Rewrote numerical instability checking for BSSVS with irreversible models -- now explicitly check the condition number of the eigenvectors

96 lines of code changed in 3 files:

bloomquist 2009-03-12 10:41 Rev.: 1492

Commented out part that didn't build correctly. Sorry for the trouble.

4 lines of code changed in 1 file:

bloomquist 2009-03-12 10:18 Rev.: 1491

Rate variation appears to be working. In fact, it seems to be working very well! For now, old arg stuff will not work, but will fix as soon as possible.

140 lines of code changed in 4 files:

msuchard 2009-03-12 05:56 Rev.: 1490

Added description of priors in UniformRootPrior and specified Bloomquist as author. Added a contouring package to remove dependency on R

1112 lines of code changed in 4 files:

msuchard 2009-03-11 10:43 Rev.: 1489

Stricter numeric stability checking on complex models

2 lines of code changed in 1 file:

rambaut 2009-03-10 05:19 Rev.: 1488

Implemented uniform root prior for dated tip trees.

28 lines of code changed in 1 file:

rambaut 2009-03-10 03:51 Rev.: 1487

Fixed issue 67: when MC3 parses its XMLs, it now stops parsing once it has found the MCMC objects. This prevents a crash when parsers after the MCMC like LogAnalysers expect log files to have been created. TraceAnalysis also behaves a bit better when the log file doesn't exist or is empty.

55 lines of code changed in 4 files:

rambaut 2009-03-10 00:45 Rev.: 1486

Fixed a problem where RandomWalkIntegerOperator wasn't accepting windowSizes that were given with decimal places even though they were integer values. This meant that XMLs created with 1.4.8 BEAUti didn't run. Now accepts decimal places but checks the value is an integer.

7 lines of code changed in 1 file:

rambaut 2009-03-10 00:38 Rev.: 1485

Fixed a 'NullPointerException' when TraceAnalysisParser was called to analyse a log file that didn't exist. Now returns a XMLParserException.

31 lines of code changed in 1 file:

bloomquist 2009-03-07 13:46 Rev.: 1484

Forgot to add these new classes.

307 lines of code changed in 3 files:

bloomquist 2009-03-07 11:46 Rev.: 1483

Not positive yet, but fairly sure have joint rate variation estimation and ARG inference working.

434 lines of code changed in 5 files:

jheled 2009-03-07 08:21 Rev.: 1482

temporary commit until sebastian sorts this out

58 lines of code changed in 7 files:

rambaut 2009-03-07 04:46 Rev.: 1481

UniformRootPrior works on trees with contemporaneous tips but not dated tips.

22 lines of code changed in 3 files:

rambaut 2009-03-07 03:00 Rev.: 1480

New Uniform Root Prior

407 lines of code changed in 4 files:

Sebastian.Hoehna 2009-03-04 10:07 Rev.: 1479

Some more work on the tree proposal operators

94 lines of code changed in 1 file:

Sebastian.Hoehna 2009-03-04 10:01 Rev.: 1478

Added some stuff to get the MGS working.

288 lines of code changed in 1 file:

Sebastian.Hoehna 2009-03-04 09:54 Rev.: 1477

Some work on convergence measurements

827 lines of code changed in 5 files:

Sebastian.Hoehna 2009-03-04 09:35 Rev.: 1476

Added a quick but dirty endTreeEdit which increases the performance of the Metropolized Gibbs Sampler by 2 even for small datasets.

15 lines of code changed in 1 file:

Sebastian.Hoehna 2009-03-04 09:16 Rev.: 1475

Some work on the tree proposal operators.

95 lines of code changed in 1 file:

Sebastian.Hoehna 2009-03-04 09:14 Rev.: 1474

Work on the new tree proposal operators. The two Metropolized Gibbs Samplers and the CCP guided samplers.

1240 lines of code changed in 4 files:

Sebastian.Hoehna 2009-03-04 09:10 Rev.: 1473

Some work on the tree proposal operators.

269 lines of code changed in 1 file:

Sebastian.Hoehna 2009-03-04 09:02 Rev.: 1472

A general framework for importance distributions by clades. It is used for the Metropolized Independence Sampler.

589 lines of code changed in 2 files:

Sebastian.Hoehna 2009-03-04 09:00 Rev.: 1471

The WMB is the method used in TreeAnnotator. I designed this class in the same way as the CCP for estimating the posterior of trees.

645 lines of code changed in 1 file:

Sebastian.Hoehna 2009-03-04 08:58 Rev.: 1470

Some work on the conditional clade frequencies.

338 lines of code changed in 3 files:

Sebastian.Hoehna 2009-03-04 08:57 Rev.: 1469

Added the new Tree Proposal Operators

353 lines of code changed in 1 file:

Sebastian.Hoehna 2009-03-03 18:31 Rev.: 1468

Error catching stuff.

6 lines of code changed in 1 file:

msuchard 2009-03-03 10:47 Rev.: 1467

Refactored to remove duplicated zero-time check in getLogLikelihood

10 lines of code changed in 2 files:

msuchard 2009-03-02 17:23 Rev.: 1466

Bug fixed; forget to add in branch-time-dependence in GreatCircle variance. oops

20 lines of code changed in 1 file:

msuchard 2009-03-02 10:07 Rev.: 1465

Added a bi-variate KDE smoother to replace call to R in annotating posterior spatial regions. This need to replace contouring on smoothed KDE

199 lines of code changed in 1 file:

msuchard 2009-03-01 21:09 Rev.: 1464

Hack in SequenceSimulator to allow epoch substitution models; to be removed when TreeBranchSiteModel issue resolved

8 lines of code changed in 1 file:

February 2009 »

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