June 2007 Commit Log

Number of Commits:
48
Number of Active Developers:
4
jheled 2007-06-29 12:01 Rev.: 345

final's and variable scope

26 lines of code changed in 1 file:

jheled 2007-06-29 11:59 Rev.: 344

Fix MixedDistributionLikelihood to work with none constant distributions. Involved changing compund likelihood to accept anothe compund as a component.

54 lines of code changed in 4 files:

jheled 2007-06-29 11:57 Rev.: 343

add 'final' and such

52 lines of code changed in 1 file:

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

ongoing work on variable dimentsion skyline

1156 lines of code changed in 19 files:

jheled 2007-06-28 16:31 Rev.: 340

code cleanup

2 lines of code changed in 1 file:

jheled 2007-06-28 16:30 Rev.: 339

add radious for better mixing

91 lines of code changed in 1 file:

jheled 2007-06-28 16:29 Rev.: 338

code cleanup

6 lines of code changed in 1 file:

jheled 2007-06-28 16:28 Rev.: 337

more comments. check for inside bounds before setting in both cases

50 lines of code changed in 1 file:

jheled 2007-06-28 16:25 Rev.: 336

comment

4 lines of code changed in 1 file:

jheled 2007-06-28 16:20 Rev.: 335

replace non-needed check with an assert. more comments

43 lines of code changed in 1 file:

jheled 2007-06-28 16:06 Rev.: 334

generify and remove dead code

20 lines of code changed in 1 file:

jheled 2007-06-28 16:05 Rev.: 333

generify

6 lines of code changed in 1 file:

alexei.drummond 2007-06-28 11:31 Rev.: 332

adding example analysis and figure

26 lines of code changed in 1 file:

rambaut 2007-06-28 03:21 Rev.: 331

More bits ported over from 1.4

3297 lines of code changed in 9 files:

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

Fixed 2 bugs in patristic distances code

37 lines of code changed in 6 files:

jheled 2007-06-26 06:02 Rev.: 327

newline at end to eliminate gcc warning

1 lines of code changed in 2 files:

jheled 2007-06-25 11:49 Rev.: 326

generify

13 lines of code changed in 1 file:

jheled 2007-06-25 11:46 Rev.: 325

minor cleanup

18 lines of code changed in 1 file:

jheled 2007-06-25 11:45 Rev.: 324

remove unused code

28 lines of code changed in 1 file:

jheled 2007-06-25 11:39 Rev.: 323

add more tree distance methods

162 lines of code changed in 2 files:

jheled 2007-06-25 11:33 Rev.: 322

generify

7 lines of code changed in 1 file:

jheled 2007-06-25 11:22 Rev.: 321

cleanup

14 lines of code changed in 1 file:

jheled 2007-06-25 11:20 Rev.: 320

generify & simplify

16 lines of code changed in 1 file:

jheled 2007-06-25 11:16 Rev.: 319

comment & generify

14 lines of code changed in 1 file:

jheled 2007-06-25 09:56

generify

74 lines of code changed in 4 files:

jheled 2007-06-25 09:55 Rev.: 314

add final modifiers

3 lines of code changed in 1 file:

jheled 2007-06-25 09:54 Rev.: 313

fix copy/paste of comments

2 lines of code changed in 1 file:

jheled 2007-06-25 09:52 Rev.: 312

simple factoring and generifying

23 lines of code changed in 1 file:

jheled 2007-06-25 09:45 Rev.: 311

add final modifier

3 lines of code changed in 1 file:

jheled 2007-06-25 09:43 Rev.: 310

chain string appends

1 lines of code changed in 1 file:

jheled 2007-06-25 09:39 Rev.: 309

comment unused code

45 lines of code changed in 1 file:

jheled 2007-06-25 09:36 Rev.: 308

fix comments

2 lines of code changed in 1 file:

jheled 2007-06-25 09:34 Rev.: 307

remove unneeded final from main

1 lines of code changed in 1 file:

jheled 2007-06-25 09:33 Rev.: 306

comments

4 lines of code changed in 2 files:

jheled 2007-06-25 09:31 Rev.: 305

non ascii in comment

3 lines of code changed in 2 files:

jheled 2007-06-25 09:28 Rev.: 304

add check for read failure

5 lines of code changed in 1 file:

jheled 2007-06-25 09:10 Rev.: 303

no perdormace suggestion for a gibbs operator

27 lines of code changed in 1 file:

alexei.drummond 2007-06-24 21:54 Rev.: 302

Okay, I have read through the text and the BEAST paper is definitely ready! Just needs a figure which I will work on right now!

92 lines of code changed in 1 file:

alexei.drummond 2007-06-24 20:39 Rev.: 301

Converted the prior types to an Enum in BEAUti and did a bit of 1.5ifying. It turned out to be a bit more work than I anticipated. BEAUti is a beast ;-)

255 lines of code changed in 7 files:

alexei.drummond 2007-06-24 19:21 Rev.: 300

Integration of Random Local Clock model into BEAUTi, plus a few improvements to TreeModel, SpeciationLikelihood and related classes

590 lines of code changed in 18 files:

gerton.lunter 2007-06-23 04:42 Rev.: 299

Test commit - no change

541 lines of code changed in 1 file:

rambaut 2007-06-21 21:11 Rev.: 298

Made a start on using tracer.

61 lines of code changed in 1 file:

gerton.lunter 2007-06-17 01:49 Rev.: 291

Changed ExponentialMarkovPrior so that it can also produce Gamma markov priors,
to control the variation of population size across groups. Default is shape=1.0
corresponding to an exponential Markov prior.

The Bayesian skyline operator can now also use this prior; as before, with matching
priors a Gibbs sampling step is obtained.

Fixed a small bug in BeastParser.

Generalized the sampling code from the biased Gamma distribution; if G(x;shape,scale,bias)
= x^(shape-1) e^(x/scale) e^(1/(bias*x)), then this distribution is normalizable for
scale>0, bias>0 and all shape parameters (including 0); the sampling code can now handle
all these cases.


99 lines of code changed in 5 files:

gerton.lunter 2007-06-11 21:55 Rev.: 290

Added <generalizedSkylineGibbsOperator> to BeastMain's parser.

Comment added to bayesianskylinegibbsoperator.java.



7 lines of code changed in 2 files:

gerton.lunter 2007-06-04 22:14 Rev.: 289

Minor bugfix

1 lines of code changed in 1 file:

gerton.lunter 2007-06-04 21:40 Rev.: 288

Cleanup of GammaDistribution.java - more straightforward algorithm to sample from a exp-weighted Gamma distribution

590 lines of code changed in 1 file:

gerton.lunter 2007-06-01 22:24 Rev.: 287

Changed the way the Gibbs sampler for the Bayesian skyline works. Instead of
sampling all population parameters at once, they are now sampled one-at-a-time
in one-dimensional Gibbs moves.

The advantage is that the exponential Markov prior can now be efficiently incorporated
- previously this prior would cause very high rejection rates (~99%), because new states
would often have a bad prior likelihood, whereas now the Gibbs move has acceptance
rate 1.

The exponential Markov prior has been updated to also 'run in reverse' if desired,
putting a Jeffrey's prior on the most ancestral Ne rather than the most recent.
The Gibbs sampler can handle both forward and backward exponential Markov priors,
with an without a Jeffrey's prior on the first (last) Ne.

The sampling code for the exponential-weighted Gamma distribution has been updated
and is more efficient.


492 lines of code changed in 3 files:

rambaut 2007-06-01 10:56 Rev.: 286

Fixed a couple of errors due to an incomplete port of fixes from the 1.4 branch.

61 lines of code changed in 2 files:

May 2007 »

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