July 2007 Commit Log

Number of Commits:
70
Number of Active Developers:
5
rambaut 2007-07-31 22:37 Rev.: 433

FrequencyModel parser now writes out what it is doing

114 lines of code changed in 1 file:

jheled 2007-07-31 19:51 Rev.: 432

fix bug (primates_twoFossil.xml)

3 lines of code changed in 1 file:

msuchard 2007-07-29 06:51 Rev.: 431

Added native (fortran) routines to approximate the exponential of huge sparse matrices. These routines will be used in random-walk on maps models, where the order of a 100 x 100 map = 10,000 and it is impractical to exponentiate the 10,000 x 10,000 rate matrix exactly. These approximations come from ExpoKit (ok to modify/distribute for non-commercial purposes) and use a Krylov-subspace approach. Also included is a good Pade approximator (which we may want to port to Java/C and use for the character substitution rate matrices). I plan to commit a working random-walk on the San Francisco Bay Area map example soon.

4887 lines of code changed in 8 files:

rambaut 2007-07-27 08:39 Rev.: 430

sortTranslationTable now defaults to true.

1 lines of code changed in 1 file:

rambaut 2007-07-26 21:28 Rev.: 429

Fixed problem logging trees MCMCMC (was giving null taxon labels).

25 lines of code changed in 3 files:

rambaut 2007-07-26 20:52 Rev.: 428

Added UI for doing marginal likelihood analyses. Actual call to analysis code is not implemented yet. May generalize this for calculating BFs between traces?

3 lines of code changed in 1 file:

alexei.drummond 2007-07-25 03:47 Rev.: 425

Allow # comments at start of log files...

18 lines of code changed in 2 files:

alexei.drummond 2007-07-25 01:37 Rev.: 424

tweaks

26 lines of code changed in 7 files:

benjamin.redelings 2007-07-23 12:37 Rev.: 421

[FIX] Allow 'ant' to build beast on linux.
* build.xml: add lib/mtj.jar to beast classpath
* build_development.xml: ditto.

95 lines of code changed in 2 files:

rambaut 2007-07-23 01:47 Rev.: 420

Added UI for doing marginal likelihood analyses. Actual call to analysis code is not implemented yet. May generalize this for calculating BFs between traces?

211 lines of code changed in 4 files:

rambaut 2007-07-23 01:18 Rev.: 419

Many fixes to Tracer - progressing to v1.4 release

396 lines of code changed in 15 files:

alexei.drummond 2007-07-22 18:30 Rev.: 418

8 lines of code changed in 4 files:

rambaut 2007-07-21 00:00 Rev.: 416

FigTree tree now has mean heights

0 lines of code changed in 1 file:

rambaut 2007-07-20 23:37 Rev.: 415

More tweaking...

122 lines of code changed in 2 files:

rambaut 2007-07-20 11:01 Rev.: 413

Fixed up the practice section according to Philippe's suggestions

190 lines of code changed in 23 files:

rambaut 2007-07-19 23:12 Rev.: 412

Possibly fixed problem with swapping loggers during MCMCMC. This compiles but is not tested - have run out of time.

115 lines of code changed in 2 files:

alexei.drummond 2007-07-19 17:35 Rev.: 411

added new move to help mixing in RLC models... might have to use MCMCMC though...

212 lines of code changed in 3 files:

msuchard 2007-07-19 11:22 Rev.: 410

0 lines of code changed in 1 file:

msuchard 2007-07-17 10:52 Rev.: 409

FIrst-pass hack at implementing a weighted random walk on a d-2 Markov lattice. Allows for discretized diffusion on a terrain (topographic) map for use with the "coyote" (errr cougar) data. The MapMaker class currently requires mtj.jar (optimized sparse matrix operations) to construct the eigensystem of the weighted lattice.

1046 lines of code changed in 9 files:

rambaut 2007-07-17 01:44 Rev.: 408

Cleaned up output of XML documentation generation for MediaWiki. This now generates a file which can be pasted into the BEAST wiki. See http://beast.bio.ed.ac.uk/BEAST_XML_Reference for current version

28 lines of code changed in 4 files:

rambaut 2007-07-17 00:42 Rev.: 407

Added F81. Fixed some references to existing papers.

518 lines of code changed in 11 files:

rambaut 2007-07-17 00:04 Rev.: 406

Adding a new figure

0 lines of code changed in 6 files:

rambaut 2007-07-17 00:00

More edits to BookSection

130 lines of code changed in 4 files:

rambaut 2007-07-16 11:36 Rev.: 403

Added the ability to create MediaWiki output to BEASTDoc - not beautiful yet.

326 lines of code changed in 11 files:

alexei.drummond 2007-07-15 00:09 Rev.: 402

many small grammatical fixes -- there was a big merge conflict because of different formats for software names -- I thought the bold was a bit intrusive.

212 lines of code changed in 1 file:

rambaut 2007-07-14 23:11 Rev.: 401

Cleaned up the BookSection a bit to make the formatting more consistent, use the more correct term 'dengue virus serotype 4', 'E' (not env) gene. Teletype style for UI components. Bold style for programs. Resized figures. Few typos.

78 lines of code changed in 1 file:

alexei.drummond 2007-07-14 18:00 Rev.: 400

I added the basic guff about Bayesian MCMC and what it is all about. The only thing missing is a proper discussion of the important role of priors...

96 lines of code changed in 1 file:

rambaut 2007-07-14 00:32 Rev.: 399

Finished up the text of the practical section. My latex is still rusty so there may be glitches.

82 lines of code changed in 1 file:

rambaut 2007-07-13 23:21 Rev.: 398

Added a few more synchronisations to allow multithreading.

16 lines of code changed in 1 file:

alexei.drummond 2007-07-12 22:51 Rev.: 396

1 lines of code changed in 3 files:

alexei.drummond 2007-07-12 22:32 Rev.: 395

Why the coalescent likelihood we currently have is right :-) (of course!)

118 lines of code changed in 2 files:

rambaut 2007-07-12 21:39 Rev.: 394

Added a few more synchronisations to allow multithreading. This includes GammaSiteModel & HKY. Basically, any lazy calculations for instance variables in functions called by TreeLikelihood need to be synchronized.

771 lines of code changed in 6 files:

alexei.drummond 2007-07-12 18:44 Rev.: 393

implemented multi-threading support for AbstractSubstitutionModel in aid of AR's work on multithreading likelihood calculations.

1050 lines of code changed in 2 files:

rambaut 2007-07-12 11:24

An experiment: Implemented multithreading in CompoundLikelihood. The idea is that all the contained likelihoods are calculated concurrently on multicore machines. This may work with multiple treelikelihoods (i.e., data partitions). To turn on, add the attribute threads="x" to the compoundLikelihood (including "posterior", "prior" and "likelihood" aliases) where x is the number of threads to use (match number of cores or number of likelihoods?) omit for no threads. This uses a thread pool implemented in ExecutorService to run the threads but spawning that many threads (i.e., each state) may have too much overhead unless there are a lot of patterns.

180 lines of code changed in 3 files:

msuchard 2007-07-12 06:54 Rev.: 390

Finished a basic implementation of the GMRF coalescent smoother. This implementation currently uses a random walk operator on the population sizes and a Gibbs update of the precision parameter. A (much) better/faster approach (to come shortly) is a joint update using Rue's GMRF library.

348 lines of code changed in 4 files:

alexei.drummond 2007-07-11 23:57 Rev.: 387

added a boolean attribute to the tree logger to optionally sort the translation table in BEAST tree files so that AWTY can be more easily used to compare independent runs...

257 lines of code changed in 2 files:

rambaut 2007-07-11 00:25 Rev.: 384

Full evaluation wasn't being set properly.

25 lines of code changed in 2 files:

rambaut 2007-07-10 23:53 Rev.: 382

Have fixed NewCoalescentLikelihood. Have replaced it as the default coalescent likelihood in BeastParser (because changes to CoalescentLikelihood seem to have broken it). Preliminary indications are that it is faster and the code is cleaner.

179 lines of code changed in 6 files:

rambaut 2007-07-10 20:52 Rev.: 379

Have made 'fullEvaluationCount' an attribute of MCMC. If not specified then it has a default of 2000 (this is now an option in MCMCOptions). Set to chain length to fully evaluate the likelihood after every restore.

27 lines of code changed in 4 files:

alexei.drummond 2007-07-10 17:01 Rev.: 378

little utility to order translation table in Nexus files so that AWTY can be used...

131 lines of code changed in 3 files:

rambaut 2007-07-10 04:13 Rev.: 377

Improved the update messages being passed from DiscretizedBranchRates to TreeLikelihood so that only those nodes that need updating do so. This shows a significant improvement in speed and gives the same sequence of likelihoods with the test XML scripts for a given seed.

32 lines of code changed in 2 files:

rambaut 2007-07-10 02:04 Rev.: 376

Added parser error when the rate category parameter is not of dimension nodeCount - 1.

4 lines of code changed in 1 file:

alexei.drummond 2007-07-09 17:49 Rev.: 375

Split TreeModel XML parser into separate class because TreeModel is a monolithic class. Fixed a labeling problem introduced into CoalescentLikelihood. However the CoalescentLikelihood now returns weird probabilities after jheled's last commit -- so this still needs looking into.

337 lines of code changed in 11 files:

msuchard 2007-07-09 13:40

200 lines of code changed in 2 files:

msuchard 2007-07-09 13:38 Rev.: 372

Attempted to fix how traits are re-created in TreeModel. testMultivariateTraits.xml is a quick demo of the multivariate Comparative Methods tools.

156 lines of code changed in 3 files:

alexei.drummond 2007-07-09 01:49 Rev.: 371

oh well not quite yet...

5 lines of code changed in 2 files:

alexei.drummond 2007-07-09 01:31 Rev.: 370

speed improvements to relaxed clocks (~20% faster to uncorrelated models) - important changes for porting are DiscretizedBranchRates and TreeLikelihood

93 lines of code changed in 7 files:

msuchard 2007-07-08 17:54 Rev.: 369

I hope I didn't just break TreeModel

1169 lines of code changed in 1 file:

msuchard 2007-07-08 17:49 Rev.: 368

528 lines of code changed in 3 files:

msuchard 2007-07-08 17:38 Rev.: 367

Added the classes below to implement the multivariate Comparative Method. Unfortunately, MultivariateTraitLikelihood no longer works with the current TreeModel with a HashMap of traitParameters.

MultivariateDiffusionModel
MultivariateTraitLikelihood
MultivariateDistributionLikelihood
InternalTraitGibbsOperator
PrecisionMatrixGibbsOperator
MultivariateDistribution
MultivariateNormalDistribution
WishartDistribution
CorrelationStatistic

2278 lines of code changed in 14 files:

msuchard 2007-07-08 17:37 Rev.: 366

84 lines of code changed in 1 file:

jheled 2007-07-08 07:27 Rev.: 365

tidyup and generifying

64 lines of code changed in 1 file:

jheled 2007-07-07 08:01 Rev.: 364

tidyup and generifying

231 lines of code changed in 26 files:

rambaut 2007-07-07 04:48 Rev.: 363

Updated practical section

307 lines of code changed in 4 files:

rambaut 2007-07-07 01:47 Rev.: 362

Moved BookSection into a folder with all its figures

782 lines of code changed in 16 files:

rambaut 2007-07-07 01:43 Rev.: 361

Updated BookSection again

244 lines of code changed in 1 file:

alexei.drummond 2007-07-06 23:09 Rev.: 360

tidying

17 lines of code changed in 1 file:

rambaut 2007-07-06 19:57 Rev.: 359

Updated book chapter

88 lines of code changed in 1 file:

jheled 2007-07-06 12:12 Rev.: 358

fix a bug which caused a crash when two coalecsent events are merged. Also add functionality for obtaining every coalecsent event as a separate event.

29 lines of code changed in 1 file:

jheled 2007-07-06 09:16 Rev.: 357

export did not work

7 lines of code changed in 1 file:

alexei.drummond 2007-07-05 16:50 Rev.: 356

346 lines of code changed in 3 files:

alexei.drummond 2007-07-05 14:18 Rev.: 355

Random Local Clocks are on there way...

151 lines of code changed in 3 files:

jheled 2007-07-04 10:24 Rev.: 354

fix calculation of indications/pops number relative to trees

46 lines of code changed in 1 file:

jheled 2007-07-04 10:23 Rev.: 353

add "method" attribute to xml rules

3 lines of code changed in 1 file:

alexei.drummond 2007-07-03 17:42 Rev.: 352

added ability to specify what posterior probability cutoff to output clades at, and also output mean height of clades in tree trace analysis

230 lines of code changed in 4 files:

alexei.drummond 2007-07-03 00:09 Rev.: 351

fixed url for Tracer, title and acknowledgements

5 lines of code changed in 3 files:

alexei.drummond 2007-07-02 18:26 Rev.: 350

and bib file...

9751 lines of code changed in 1 file:

alexei.drummond 2007-07-02 18:25 Rev.: 349

final draft of manuscript?

30 lines of code changed in 1 file:

jheled 2007-07-02 16:20 Rev.: 348

Issue a warning for attributes of elements in BEAST xml files which are not declared by the XML rules. This helps both users (like me) not to get stung by silent ignore of typos, and developers (like me) which need to debug rules for new elements.

Those changes involves fixing some elements rules, and additional cleanup.

327 lines of code changed in 27 files:

alexei.drummond 2007-07-02 11:58 Rev.: 346

Updated manuscript and manual and cleaned up a bit of lint...

1926 lines of code changed in 11 files:

June 2007 »

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