StatSVN - Directory src/dr/inferencexml/

[root]/src/dr/inferencexml

distribution (26 files, 1353 lines)

loggers (3 files, 101 lines)

model (32 files, 1527 lines)

operators (31 files, 1316 lines)

trace (6 files, 436 lines)

Author	Changes	Lines of Code	Lines per Change
Totals	59 (100.0%)	2884 (100.0%)	48.8
sibon.li	6 (10.2%)	1197 (41.5%)	199.5
alexei.drummond	6 (10.2%)	920 (31.9%)	153.3
dong.w.xie	22 (37.3%)	492 (17.1%)	22.3
msuchard	11 (18.6%)	137 (4.8%)	12.4
rambaut	7 (11.9%)	116 (4.0%)	16.5
jheled	6 (10.2%)	20 (0.7%)	3.3
julia.pal.r@gmail.com	1 (1.7%)	2 (0.1%)	2.0

Most Recent Commits

rambaut 2012-08-11 08:53 Rev.: 5122

Fix for Issue 655: Operator log sometimes attempts to write to locked folder causing exception. Needs testing and porting to 1.7 branch.

3 lines of code changed in 2 files:

src/dr/inferencexml: MCMCParser.java (+3 -1)

sibon.li 2012-04-07 06:46 Rev.: 4920

Added an interface for delegating tasks in the Markov Chain

16 lines of code changed in 1 file:

src/dr/inferencexml: MCMCParser.java (+16 -3)

msuchard 2012-03-07 12:09 Rev.: 4780

Reverting inadvertent changes from Julia

4 lines of code changed in 1 file:

src/dr/inferencexml: MCMCParser.java (+4 -6)

julia.pal.r@gmail.com 2012-03-07 11:42 Rev.: 4779

Not finished but descent version of GPOperator - fixing imports :S

2 lines of code changed in 1 file:

src/dr/inferencexml: MCMCParser.java (+2)

rambaut 2012-03-04 01:01 Rev.: 4761

Removing wrongly located files.

0 lines of code changed in 1 file:

src/dr/inferencexml: BlueBeastMCMCParser.java (del)

sibon.li 2012-03-03 21:38 Rev.: 4758

Commented out all of my last commit until issues resolved

294 lines of code changed in 1 file:

src/dr/inferencexml: BlueBeastMCMCParser.java (new 294)

sibon.li 2012-03-03 18:40 Rev.: 4757

Test build

1 lines of code changed in 1 file:

src/dr/inferencexml: BlueBeastMCMCParser.java (+1 -1)

sibon.li 2012-03-03 16:23 Rev.: 4755

Added classes to enable implicit convergence assessment checks using BLUE

294 lines of code changed in 1 file:

src/dr/inferencexml: BlueBeastMCMCParser.java (+294 -294)

sibon.li 2012-02-28 12:09 Rev.: 4743

Correction, parsers pending updates to other files. Currently commented out

294 lines of code changed in 1 file:

src/dr/inferencexml: BlueBeastMCMCParser.java (+294 -294)

sibon.li 2012-02-28 12:05 Rev.: 4742

Added two new parsers for BLUE integration

298 lines of code changed in 1 file:

src/dr/inferencexml: BlueBeastMCMCParser.java (+298)

rambaut 2011-11-15 09:26 Rev.: 4424

Upgraded chain length to a 64 bit integer so that chain lengths > 2.1 billion can be done. This addresses issue 540. Runs OK, accepts long chain lengths but not actually tested a run of > 2.1 billion.

5 lines of code changed in 1 file:

src/dr/inferencexml: MCMCParser.java (+5 -5)

rambaut 2010-06-12 03:51 Rev.: 3252

Prettied-up the printing of diagnostic message for a zero initial likelihood (actually this is a port of a improvement from the BEAST v1.5.x branch).

1 lines of code changed in 1 file:

src/dr/inferencexml: MCMCParser.java (+1 -1)

rambaut 2010-06-07 23:59 Rev.: 3236

Normalized the naming of a few classes and added a note in the MCMC parser to say if the fullEvaluation has been turned off.

4 lines of code changed in 1 file:

src/dr/inferencexml: MCMCParser.java (+4 -2)

dong.w.xie 2010-03-02 10:05 Rev.: 3001

Trunk refactoring: finish MCMC (split parsers).

243 lines of code changed in 2 files:

src/dr/inferencexml: MCMCParser.java (+175), MLOptimizerParser.java (new 68)

dong.w.xie 2010-02-25 15:52 Rev.: 2982

Trunk refactoring: organize distribution parsers again.

0 lines of code changed in 6 files:

src/dr/inferencexml: BinomialLikelihoodParser.java (del), CachedDistributionLikelihoodParser.java (del), DuplicatedParameterParser.java (del), LikelihoodBenchmarkerParser.java (del), MaskedParameterParser.java (del), PriorParsers.java (del)

dong.w.xie 2010-02-25 13:51 Rev.: 2979

Trunk refactoring: organize distribution parsers.

0 lines of code changed in 7 files:

src/dr/inferencexml: DistributionLikelihoodParser.java (del), DistributionModelParser.java (del), EmpiricalDistributionLikelihoodParser.java (del), ExponentialDistributionModelParser.java (del), ExponentialMarkovModelParser.java (del), GammaDistributionModelParser.java (del), OnePGammaDistributionModelParser.java (del)

msuchard 2010-02-24 03:36 Rev.: 2962

Fixed jitter for IntegratedMultivariateTraitLikelihood

1 lines of code changed in 1 file:

src/dr/inferencexml: OnePGammaDistributionModelParser.java (new 1)

dong.w.xie 2010-02-17 14:56 Rev.: 2931

Trunk refactoring: complex substitution model (split parsers).

104 lines of code changed in 2 files:

src/dr/inferencexml: DuplicatedParameterParser.java (new 49), MaskedParameterParser.java (new 55)

dong.w.xie 2010-02-16 13:42 Rev.: 2923

Trunk: make all parsers loaded properly, from now, BeastParser only allow to keep very basic xml parsers.

102 lines of code changed in 4 files:

src/dr/inferencexml: DistributionModelParser.java (new), ExponentialDistributionModelParser.java (new 34), GammaDistributionModelParser.java (new 34), OnePGammaDistributionModelParser.java (+34)

msuchard 2009-12-22 12:15 Rev.: 2714

Working on arbitrary branch rates for a real scaled mixture of normals

6 lines of code changed in 1 file:

src/dr/inferencexml: PriorParsers.java (new 6)

msuchard 2009-11-11 15:00 Rev.: 2529

Empiricial distributions can now take an offset in the <data> block

7 lines of code changed in 1 file:

src/dr/inferencexml: EmpiricalDistributionLikelihoodParser.java (new 7)

jheled 2009-10-26 07:45 Rev.: 2464

make attribute optional

2 lines of code changed in 1 file:

src/dr/inferencexml: PriorParsers.java (+2 -2)

jheled 2009-10-07 13:22 Rev.: 2354

remove unused attribute

1 lines of code changed in 1 file:

src/dr/inferencexml: PriorParsers.java (+1 -1)

msuchard 2009-10-06 06:04 Rev.: 2349

Fixes to CachedDistributionLikelihood to work with MultivariateDistributionLikelihood. Tweaks to eigendecomposition routines, in case of invalid diagonalization

6 lines of code changed in 1 file:

src/dr/inferencexml: CachedDistributionLikelihoodParser.java (new 6)

msuchard 2009-09-24 13:09 Rev.: 2284

Parsing for spline-interpolated empirical (prior) distributions appears to work.

7 lines of code changed in 1 file:

src/dr/inferencexml: EmpiricalDistributionLikelihoodParser.java (+7 -2)

dong.w.xie 2009-09-16 12:14 Rev.: 2254

BEAUTi:
1) solve Issue 135: Laplace prior has not been implemented in PriorParsers, but appearing in BEAUTi;
2) solve Issue 158: We should have the Inverse Gamma distribution in Beauti.

43 lines of code changed in 1 file:

src/dr/inferencexml: PriorParsers.java (+43)

jheled 2009-09-08 06:36 Rev.: 2221

automatic idea changes and generify

7 lines of code changed in 1 file:

src/dr/inferencexml: PriorParsers.java (+7 -7)

jheled 2009-09-07 13:29 Rev.: 2212

auto intelliJ

1 lines of code changed in 1 file:

src/dr/inferencexml: DistributionLikelihoodParser.java (new 1)

jheled 2009-09-04 10:29 Rev.: 2195

code police

3 lines of code changed in 1 file:

src/dr/inferencexml: PriorParsers.java (+3 -3)

jheled 2009-08-17 16:57 Rev.: 2089

MIndless cleanup

6 lines of code changed in 1 file:

src/dr/inferencexml: CachedDistributionLikelihoodParser.java (+6 -6)

msuchard 2009-08-16 10:50 Rev.: 2079

Added a wrapper around a DistributionLikelihood such that its likelihood is only recomputed after a handleVariableChangedEvent; this results in substantial speed-up for models with priors on parameter with high dimension (such as 100s or 1000s)

58 lines of code changed in 2 files:

src/dr/inferencexml: CachedDistributionLikelihoodParser.java (+57), DistributionLikelihoodParser.java (+1 -1)

msuchard 2009-07-29 04:42 Rev.: 1938

Added a one-parameter Gamma distribution parser (a la Yang's rate model and for scaled mixtures of normals).

It would be nice to have a way to overload parsers in DistributionModelParser without having to give new names

26 lines of code changed in 1 file:

src/dr/inferencexml: DistributionModelParser.java (+26)

msuchard 2009-07-28 11:40 Rev.: 1935

Implemented linear interpolation in EmpiricalDistributionLikelihood for use with John's problem.

6 lines of code changed in 1 file:

src/dr/inferencexml: EmpiricalDistributionLikelihoodParser.java (+6 -2)

msuchard 2009-07-20 15:52 Rev.: 1881

Connecting SplineBasis and EmpiricalDistributionLikelihood so Andrew can get this all working while I am gone. And, I used Variables<Double> ... good on me!

16 lines of code changed in 1 file:

src/dr/inferencexml: EmpiricalDistributionLikelihoodParser.java (+16 -1)

rambaut 2009-07-17 05:37 Rev.: 1865

Added the husk of a likelihood function that provides a density based on a (smoothed) function provided by a file of data. This is for some stuff that Marc, John and Andrew are working on. Compiles but doesn't function yet.

103 lines of code changed in 1 file:

src/dr/inferencexml: EmpiricalDistributionLikelihoodParser.java (+103)

alexei.drummond 2009-07-17 01:13 Rev.: 1863

Beginning of refactoring to remove dr.inference.* dependency on dr.xml. Will take a while...

920 lines of code changed in 6 files:

src/dr/inferencexml: BinomialLikelihoodParser.java (new 85), DistributionLikelihoodParser.java (+106), DistributionModelParser.java (+146), ExponentialMarkovModelParser.java (new 94), LikelihoodBenchmarkerParser.java (new 89), PriorParsers.java (+400)

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