StatSVN - Directory src/dr/app/beastdev/

Author	Changes	Lines of Code	Lines per Change
Totals	60 (100.0%)	1838 (100.0%)	30.6
msuchard	15 (25.0%)	967 (52.6%)	64.4
rambaut	21 (35.0%)	548 (29.8%)	26.0
alexei.drummond	13 (21.7%)	273 (14.9%)	21.0
jheled	8 (13.3%)	46 (2.5%)	5.7
bloomquist	2 (3.3%)	3 (0.2%)	1.5
gerton.lunter	1 (1.7%)	1 (0.1%)	1.0

Most Recent Commits

rambaut 2008-03-29 05:06 Rev.: 791

As I threatened, I have now deleted dr.app.beastdev (I had one yes and no complaints).

0 lines of code changed in 4 files:

src/dr/app/beastdev: BeastMC3.java (del), BeastMain.java (del), BeastParser.java (del), BeastVersion.java (del)

rambaut 2008-03-28 23:02 Rev.: 790

A bit more cleaning up. AbstractCoalescentLikelihood is now called OldAbstractCoalescentLikelihood to indicate to authors of descendent classes that they may wish to try and use the new "AbstractCoalescentLikelihood" which is cleaner and more modular. It also allows for <include> and <exclude> of taxon lists to do subtrees. Basically, all subclasses have to do is implement calculateLogLikelihood() and call getIntervals() and getTree() to get the current intervals and tree objects. See "CoalescentLikelihood" for an example (also the parser for including and excluding taxon lists - otherwise provide nulls).

12 lines of code changed in 2 files:

src/dr/app/beastdev: BeastParser.java (+12 -9)

rambaut 2008-03-28 01:49 Rev.: 785

I have renamed 'NewCoalescentLikelihood' as 'CoalescentLikelihood' to clarify things a bit. NewCoalescentLikelihood was more efficient and clean implementation and it's parser was installed as the default 'coalescentLikelihood' anyway since BEAST v1.4.x.

I have renamed 'CoalescentLikelihood' to AbstractCoalescentLikelihood and removed the parser (made it abstract). This class is used as a base by a number of other classes (i.e., BayesianSkylineLikelihood). I guess that ideally, we see what of AbstractCoalescentLikelihood the descendents actually use and strip out some of it.

1 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+1)

bloomquist 2008-03-26 05:51 Rev.: 782

Changed remaining skyline's to skyride's to match up with Minin et al. resubmission.

2 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+2 -2)

bloomquist 2008-03-26 05:47 Rev.: 781

Renamed GMRFSkylineLikelihood to GMRFSkyrideLikelihood to match up with Minin et al. resubmission.

1 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+1 -1)

rambaut 2008-03-26 03:22 Rev.: 780

An error in the BeastParser - some parsers were included twice

0 lines of code changed in 1 file:

src/dr/app/beastdev: BeastMC3.java (del)

rambaut 2008-03-21 04:24 Rev.: 773

Updated dr.app.beast.BeastParser to contain all the parsers in dr.app.beastdev.*. Will delete dr.app.beastdev.* soon. Moved BeastMC3 across. Fixed a bug setting BSP group count in Beauti.

219 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+219 -221)

jheled 2008-02-25 15:55 Rev.: 722

add nee 1994 birth/death model. fix likelihood calculation by adding the ignored "tree probability".

3 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+3 -1)

rambaut 2008-02-01 02:01 Rev.: 678

Fixed issue 39

5 lines of code changed in 2 files:

src/dr/app/beastdev: BeastMain.java (+5)

jheled 2008-01-15 10:45 Rev.: 667

variable demographic stuff

15 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+15 -5)

rambaut 2008-01-09 12:21 Rev.: 652

Various improvements to BEAUti and the odd bit of cleaning up. Some additions to tracer

239 lines of code changed in 1 file:

src/dr/app/beastdev: BeastMC3.java (new 239)

msuchard 2007-12-10 12:46 Rev.: 634

Added generalized GTR model with separate root and stationary distributions for irreversible processes. Added a Dirchlet prior distribution for informative root or stationary distributions. NodeTraitLogger just annotates trees with all traits.

4 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+4 -2)

msuchard 2007-11-29 12:30 Rev.: 627

Started an InhibitionAssayLikelihood class for combining inhibition assay data with phylogenetic reconstruction

6 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+6 -2)

rambaut 2007-11-15 12:35 Rev.: 591

Moved some evolution specific operators from dr.inference.operators to dr.evomodel.operators (all Marc's I think).

5 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+5 -4)

msuchard 2007-11-12 13:28 Rev.: 583

Started a MultivariateGammaDistribution for specifying pairwise distance-based rates for the discrete CTMC diffusion models.

1 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+1)

msuchard 2007-10-31 04:08 Rev.: 579

Started to add in classes for a multivate OU diffusion process and using Beast for doing (generalized) linear regression problems. May Beast become the new WinBugs!

11 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+11 -4)

msuchard 2007-10-04 16:00 Rev.: 565

5 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+5)

msuchard 2007-09-28 01:41 Rev.: 554

Add a version of the general time-reversible CTMC that employs Bayesian stochastic variable selection to choose the appropriate number of free parameters. There are still some issues with priors/normalization to be worked out, but otherwise -- LET'S WRITE A PAPER!

BitFlipInSubstitutionModelOperator is only necessary if one wants to mandate an irreducible chain, otherwise BitFlipOperator works fine and almost surely returns irreducible chains.

4 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+4)

rambaut 2007-09-27 04:25 Rev.: 548

Moved Marc's stuff into BEAST parser

0 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (-5)

msuchard 2007-09-27 03:16 Rev.: 547

Map stuff

215 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+215 -209)

msuchard 2007-08-14 12:59 Rev.: 499

Started Gibbs operator for fixed effects in the GMRF

1 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+1 -1)

alexei.drummond 2007-08-11 22:35 Rev.: 491

still working on genrea dna covarion model -- the parameters seem to be in the wrong cells of the matrix...

3 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+3 -3)

alexei.drummond 2007-08-11 19:49 Rev.: 489

implemented general DNA covarion models - untested!

1 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+1 -1)

msuchard 2007-08-11 06:34 Rev.: 487

207 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+207 -208)

msuchard 2007-08-11 06:25 Rev.: 486

Extended TreeLikelihood to AncestralStateTreeLikelihood. This class provides an ancestral reconstruction of the internal node states when the tree is logged. The class implements NodeAttribute(something) and performs a pre-traversal order simulation of the internal node states. To save on computations, I added a few public accessors to AbstractLikelihoodCore; these should probably be moved elsewhere, as they may conflict with the native likelihoodCores. There's a simple example in testAncestralReconstruction.xml. TreeAnnotator will need some patching to return the modal internal node states.

I apologize if ancestral reconstruction is already handled elsewhere, but in my defense, I could not find it!

BEAST users will probably enjoy doing lots of reconstruction, so let's write some sort of quick paper to inform users.

208 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+208 -206)

msuchard 2007-08-10 10:01 Rev.: 481

Removed dependence on colt by using sparse matrix algorithms in mtj, results in several order of magnitude speed increase.

9 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+9 -8)

rambaut 2007-08-09 01:16 Rev.: 473

Cleaned up all the expression statistics (mainly porting from 1.4 branch)

10 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+10 -9)

alexei.drummond 2007-08-08 21:50 Rev.: 469

tidying

244 lines of code changed in 1 file:

src/dr/app/beastdev: BeastMC3.java (+244 -239)

msuchard 2007-08-07 08:37 Rev.: 458

Starting to implement Rue's block updator for the GMRF classes

204 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+204 -203)

alexei.drummond 2007-08-06 20:16 Rev.: 448

tidying work towards improving log outputs

0 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (-1)

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

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

1 lines of code changed in 1 file:

src/dr/app/beastdev: BeastMC3.java (+1 -1)

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.

2 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+2)

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.

6 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+6 -2)

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.

2 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+2 -1)

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

1 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+1)

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

84 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+84 -75)

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

tidyup and generifying

1 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+1)

jheled 2007-06-28 16:34 Rev.: 341

ongoing work on variable dimentsion skyline

6 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+6 -1)

alexei.drummond 2007-06-26 23:42 Rev.: 328

Fixed 2 bugs in patristic distances code

3 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+3 -1)

gerton.lunter 2007-05-18 10:51 Rev.: 269

The rest of the previous commit -- parser for the bayesian skyline gibbs sampler,
and additions to the gamma distribution.

1 lines of code changed in 1 file:

src/dr/app/beastdev: BeastParser.java (+1)

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