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julia.pal.r@gmail.com 2013-05-09 05:42 Rev.: 5641

Latest version with new operator for joint--TODO: let Parameters.restore for vectors with different sizes. Tracer analysis doesn't read log files with {num,num,..}

1186 lines of code changed in 10 files:

• src/dr/app/beast: development_parsers.properties (new)
• src/dr/evomodel/coalescent: GPSkytrackAnalysis.java (+39 -21), GaussianProcessSkytrackLikelihood.java (+90 -157)
• src/dr/evomodel/coalescent/operators: GaussianProcessSkytrackBlockUpdateOperator.java (new), GaussianProcessSkytrackTreeOperator.java (new 736)
• src/dr/evomodelxml/coalescent/operators: GaussianProcessSkytrackTreeOperatorParser.java (new 117)

julia.pal.r@gmail.com 2013-03-29 13:12 Rev.: 5554

update ready for Marc to show me

90 lines of code changed in 1 file:

• src/dr/evomodel/coalescent: GaussianProcessSkytrackLikelihood.java (+90 -9)

julia.pal.r@gmail.com 2013-03-29 05:26 Rev.: 5553

adding elements to store-restore

44 lines of code changed in 3 files:

• src/dr/evomodel/coalescent: GPSkytrackAnalysis.java (+1), GaussianProcessSkytrackLikelihood.java (+41 -38)
• src/dr/evomodel/coalescent/operators: GaussianProcessSkytrackBlockUpdateOperator.java (+2)

julia.pal.r@gmail.com 2013-03-26 06:36 Rev.: 5542

small change

23 lines of code changed in 2 files:

• src/dr/evomodel/coalescent: GPSkytrackAnalysis.java (+20 -18)
• src/dr/evomodel/coalescent/operators: GaussianProcessSkytrackBlockUpdateOperator.java (+3 -2)

julia.pal.r@gmail.com 2013-03-23 09:39 Rev.: 5531

Complete phase1

24 lines of code changed in 1 file:

• src/dr/evomodel/coalescent: GPSkytrackAnalysis.java (+24 -107)

julia.pal.r@gmail.com 2013-03-23 07:40 Rev.: 5530

working on summary - need to calculate "sigmoidal" medians, etc

148 lines of code changed in 6 files:

• src/dr/evomodel/coalescent: GPSkytrackAnalysis.java (+85 -61)
• src/dr/evomodel/coalescent/operators: GaussianProcessSkytrackBlockUpdateOperator.java (+59)
• src/dr/evomodelxml/coalescent: GPSkytrackAnalysisParser.java (+1 -1)
• src/dr/evomodelxml/coalescent/operators: GaussianProcessSkytrackBlockUpdateOperatorParser.java (new)

julia.pal.r@gmail.com 2013-03-23 04:33 Rev.: 5529

added the "tracer" analysis similar to EBSP

495 lines of code changed in 7 files:

• src/dr/app/beast: development_parsers.properties (+1)
• src/dr/evomodel/coalescent: GPSkytrackAnalysis.java (+361), GaussianProcessSkytrackLikelihood.java (+16 -13)
• src/dr/evomodel/coalescent/operators: GaussianProcessSkytrackBlockUpdateOperator.java (+1 -1)
• src/dr/evomodelxml/coalescent: GPSkytrackAnalysisParser.java (+100), GaussianProcessSkytrackLikelihoodParser.java (new)

julia.pal.r@gmail.com 2013-03-21 05:55 Rev.: 5517

Special logger

49 lines of code changed in 3 files:

• src/dr/evomodel/coalescent: GaussianProcessSkytrackLikelihood.java (+10 -3)
• src/dr/evomodel/coalescent/operators: GaussianProcessSkytrackBlockUpdateOperator.java (+28 -3)
• src/dr/evomodelxml/coalescent: GaussianProcessSkytrackLikelihoodParser.java (+11 -1)

julia.pal.r@gmail.com 2013-03-19 05:49 Rev.: 5505

works -fixed Slice sampling detail

126 lines of code changed in 1 file:

• src/dr/evomodel/coalescent/operators: GaussianProcessSkytrackBlockUpdateOperator.java (+126 -5)

julia.pal.r@gmail.com 2013-03-19 03:57 Rev.: 5504

a working version for fixed genealogy

19 lines of code changed in 1 file:

• src/dr/evomodel/coalescent/operators: GaussianProcessSkytrackBlockUpdateOperator.java (+19 -144)

julia.pal.r@gmail.com 2013-03-17 23:27 Rev.: 5494

like GibbsOperator --not the right thing to do but temporal solution

74 lines of code changed in 2 files:

• src/dr/evomodel/coalescent: GaussianProcessSkytrackLikelihood.java (+16 -3)
• src/dr/evomodel/coalescent/operators: GaussianProcessSkytrackBlockUpdateOperator.java (+58 -28)

julia.pal.r@gmail.com 2013-03-16 06:09 Rev.: 5493

updating

13 lines of code changed in 1 file:

• src/dr/evomodel/coalescent/operators: GaussianProcessSkytrackBlockUpdateOperator.java (+13 -9)

julia.pal.r@gmail.com 2013-03-16 04:37 Rev.: 5492

just updating - need to see why infty in SliceSampler. It fails in Oldscore vs currentScore

49 lines of code changed in 2 files:

• src/dr/evomodel/coalescent: GaussianProcessSkytrackLikelihood.java (+2 -2)
• src/dr/evomodel/coalescent/operators: GaussianProcessSkytrackBlockUpdateOperator.java (+47 -43)

julia.pal.r@gmail.com 2013-03-15 15:48 Rev.: 5490

Parameterizing a lot and changes in number of latents, location of latents..need to fix GP sampling of one point, problem with "last" neighbor

376 lines of code changed in 3 files:

• src/dr/evomodel/coalescent: GaussianProcessSkytrackLikelihood.java (+85 -33)
• src/dr/evomodel/coalescent/operators: GaussianProcessSkytrackBlockUpdateOperator.java (+232 -93)
• src/dr/evomodelxml/coalescent: GaussianProcessSkytrackLikelihoodParser.java (+59 -3)

julia.pal.r@gmail.com 2013-03-13 05:50 Rev.: 5479

fixed coalescent interval in Likelihood suff. stat and small testing to Block Update

33 lines of code changed in 2 files:

• src/dr/evomodel/coalescent: GaussianProcessSkytrackLikelihood.java (+5 -1)
• src/dr/evomodel/coalescent/operators: GaussianProcessSkytrackBlockUpdateOperator.java (+28 -20)

julia.pal.r@gmail.com 2013-03-12 06:39 Rev.: 5475

Fixed updating the likelihood

9 lines of code changed in 1 file:

• src/dr/evomodel/coalescent: GaussianProcessSkytrackLikelihood.java (+9 -4)

julia.pal.r@gmail.com 2013-03-06 06:39 Rev.: 5471

added prior of hyperparameters to "likelihood" wrong but functional, don't want to add a Parser for a mixture prior

17 lines of code changed in 1 file:

• src/dr/evomodel/coalescent: GaussianProcessSkytrackLikelihood.java (+17 -3)

julia.pal.r@gmail.com 2013-03-03 11:11 Rev.: 5464

testing GPBlockUpdate -trying to understand Prior value

349 lines of code changed in 3 files:

• src/dr/evomodel/coalescent: GaussianProcessSkytrackLikelihood.java (+15 -17)
• src/dr/evomodel/coalescent/operators: GaussianProcessSkytrackBlockUpdateOperator.java (+333 -358)
• src/dr/evomodelxml/coalescent/operators: GaussianProcessSkytrackBlockUpdateOperatorParser.java (+1)

julia.pal.r@gmail.com 2013-03-02 12:56 Rev.: 5463

small changes

5 lines of code changed in 1 file:

• src/dr/evomodelxml/coalescent/operators: GaussianProcessSkytrackBlockUpdateOperatorParser.java (+5 -5)

julia.pal.r@gmail.com 2013-03-02 08:02 Rev.: 5462

small changes

48 lines of code changed in 1 file:

• src/dr/evomodel/coalescent: GaussianProcessSkytrackLikelihood.java (+48 -40)

(18 more)