/trunk Developers: bloomquist

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bloomquist 2010-03-19 08:57 Rev.: 3057

Updated getInverseIntensity() so that when growthRate = 0, it matches up with getIntensity().

4 lines of code changed in 2 files:

• src/dr/evolution/coalescent: CataclysmicDemographic.java (+4)

bloomquist 2010-03-18 12:58 Rev.: 3053

Finished up getInverseIntensity() for the CataclysmicDemographic model. Checked against getIntensity() so that getInverseIntensity(getIntensity(t)) = t. This occurs.

13 lines of code changed in 1 file:

• src/dr/evolution/coalescent: CataclysmicDemographic.java (+13 -1)

bloomquist 2009-11-19 07:39 Rev.: 2551

A few of the classes were using TREE_FILE_NAME string from some of the classes I deleted. I moved this String into STARBEASTOptions and made the appropriate changes. I don't think BEAST will be broken anymore after this.

15 lines of code changed in 3 files:

• src/dr/app/beauti/generator: LogGenerator.java (+4 -4)
• src/dr/app/beauti/mcmcpanel: MCMCPanel.java (+7 -6)
• src/dr/app/beauti/options: STARBEASTOptions.java (+4 -2)

bloomquist 2009-11-19 06:09 Rev.: 2548

Removed some obsolete classes from the dr.evomodel.coalescent package. These were loggers that were used to obtain the population sizes at fixed points in time. The use of a simple statistic however, is much easier and fits into logging framework in a smooth fashion. Thus, I have decided to tame the beast and remove some extraneous code. If these are needed at a later date, one can always check out a previous revision.

Have also updated the release_parsers.properties to remove these parsers.

3 lines of code changed in 6 files:

• src/dr/app/beast: release_parsers.properties (+2 -3)
• src/dr/evomodel/coalescent: AbstractFixedGridLogger.java (del), BayesianSkylineFixedGridLogger.java (del), GMRFFixedGridImportanceSampler.java (del), GMRFSkyrideFixedGridLogger.java (del), GMRFSkyrideLikelihood.java (+1 -1)

bloomquist 2009-11-17 14:53 Rev.: 2540

Added in a statistic for the Generalized Skyline. The statistic returns the time slice of the the skyline for a given time. If the time is beyond the root height, the statistic return Double.NaN.

76 lines of code changed in 2 files:

• src/dr/app/beast: release_parsers.properties (+1)
• src/dr/evomodel/coalescent: BayesianSkylinePopSizeStatistic.java (+75)

bloomquist 2009-10-14 09:46 Rev.: 2390

Lowered the number of stochastic tests for the gamma distribution.

1 lines of code changed in 1 file:

• src/test/dr/distibutions: GammaDistributionTest.java (+1 -1)

bloomquist 2009-10-14 09:25 Rev.: 2389

Commented my code.

11 lines of code changed in 1 file:

• src/test/dr/distibutions: GammaDistributionTest.java (+11 -1)

bloomquist 2009-10-14 08:57 Rev.: 2388

Changed the gamma distribution function test to use stochastic draws from the distribution.

5 lines of code changed in 1 file:

• src/test/dr/distibutions: GammaDistributionTest.java (+5 -57)

bloomquist 2009-10-14 08:41 Rev.: 2387

Lowered the margin of error for the JUNIT test.

1 lines of code changed in 1 file:

• src/test/dr/distibutions: GammaDistributionTest.java (+1 -1)

bloomquist 2009-10-14 08:24 Rev.: 2386

Wrote a JUNIT test for the pdf of the gamma distribution.

94 lines of code changed in 1 file:

• src/test/dr/distibutions: GammaDistributionTest.java (+94)

bloomquist 2009-05-01 07:30 Rev.: 1657

Someone changed <prec> to <precision>. Adjusted the examples accordingly.

18 lines of code changed in 3 files:

• examples: arg-ecoli.xml (new 6), arg-lepto.xml (new 6), arg-rokas.xml (new 6)

bloomquist 2009-05-01 07:15 Rev.: 1656

Made the AddRemoveOperator backwards compatible for the rate variation stuff.

33 lines of code changed in 1 file:

• src/dr/evomodel/arg/operators: ARGAddRemoveEventOperator.java (+33 -14)

bloomquist 2009-03-12 10:41 Rev.: 1492

Commented out part that didn't build correctly. Sorry for the trouble.

4 lines of code changed in 1 file:

• src/test/dr/evomodel/arg/operators: ARGAddRemoveOperatorTest.java (+4 -4)

bloomquist 2009-03-12 10:18 Rev.: 1491

Rate variation appears to be working. In fact, it seems to be working very well! For now, old arg stuff will not work, but will fix as soon as possible.

140 lines of code changed in 4 files:

• src/dr/evomodel/arg: ARGModel.java (+90 -2), ARGRatePrior.java (+17 -14)
• src/dr/evomodel/arg/operators: ARGAddRemoveEventOperator.java (+30 -19)
• src/dr/math: MathUtils.java (+3)

bloomquist 2009-03-07 13:46 Rev.: 1484

Forgot to add these new classes.

307 lines of code changed in 3 files:

• src/dr/evomodel/arg: ARGRatePrior.java (+176), ARGRelaxedClock.java (+117)
• src/dr/evomodel/arg/operators: ARGAddRemoveEventOperator.java (+14 -3)

bloomquist 2009-03-07 11:46 Rev.: 1483

Not positive yet, but fairly sure have joint rate variation estimation and ARG inference working.

434 lines of code changed in 5 files:

• src/dr/app/beast: development_parsers.properties (+2)
• src/dr/evomodel/arg: ARGModel.java (+390 -346), ARGTree.java (+16 -9)
• src/dr/evomodel/arg/likelihood: ARGLikelihood.java (+5 -2)
• src/dr/evomodel/arg/operators: ARGAddRemoveEventOperator.java (+21 -4)

bloomquist 2009-01-28 13:33 Rev.: 1413

Fixed bug when Alexei added in variable stuff to parameter changed events. Our GMRFSkyrideLikelihood never handled these new events.

3 lines of code changed in 1 file:

• src/dr/evomodel/coalescent: GMRFSkyrideLikelihood.java (+3)

bloomquist 2009-01-13 10:35 Rev.: 1409

Three example arg datasets.

10494 lines of code changed in 3 files:

• examples: arg-ecoli.xml (+778), arg-lepto.xml (+1060), arg-rokas.xml (+8656)

bloomquist 2009-01-07 15:19 Rev.: 1403

Ok, I think I got it! This one actually sampled correctly.

25 lines of code changed in 1 file:

• src/dr/evomodel/arg/operators: ARGAddRemoveEventOperator.java (+25 -16)

bloomquist 2009-01-07 13:16 Rev.: 1402

Let in some debug stuff on accident.

5 lines of code changed in 1 file:

• src/dr/evomodel/arg/operators: ARGAddRemoveEventOperator.java (+5 -10)

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