/trunk Developers: jheled

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jheled 2011-06-08 18:24 Rev.: 4016

Re-organize calibration code. add experimental "approximate" marginal.

405 lines of code changed in 7 files:

• src/dr/evomodel/speciation: BirthDeathGernhard08Model.java (+75 -61), CalibrationPoints.java (+286), SpeciationLikelihood.java (+12 -48), SpeciationModel.java (+10 -10), UltrametricSpeciationModel.java (+7 -58)
• src/dr/evomodelxml/speciation: SpeciationLikelihoodParser.java (+15 -32)

jheled 2011-06-07 11:24 Rev.: 4014

add some expectations

32 lines of code changed in 12 files:

• examples/release/calibrations: test_5t_1c_unif.xml (new), test_5t_2c_e2.xml (+5), test_5t_2c_fp_unif.xml (+5), test_5t_5c_unif.xml (new), test_7t_2c_4c_unif.xml (new), test_7t_2c_7c_unif.xml (new)

jheled 2011-06-06 17:10 Rev.: 4012

add a few calibration test files

722 lines of code changed in 7 files:

• examples/release/calibrations: test_5t_1c-pointSyntax.xml (new 97), test_5t_1c_unif.xml (+95), test_5t_2c_e2.xml (+101), test_5t_2c_fp_unif.xml (+98), test_5t_5c_unif.xml (+101), test_7t_2c_4c_unif.xml (+122), test_7t_2c_7c_unif.xml (+108)

jheled 2011-06-06 13:56 Rev.: 4011

add all worked out closed form calibration marginals: parent of clade, two nested clades, clade and root.

168 lines of code changed in 5 files:

• src/dr/evomodel/speciation: BirthDeathGernhard08Model.java (+45 -38), SpeciationLikelihood.java (+23 -15), SpeciationModel.java (+5 -4), UltrametricSpeciationModel.java (+29 -14)
• src/dr/evomodelxml/speciation: SpeciationLikelihoodParser.java (+66 -16)

jheled 2011-05-23 12:24 Rev.: 3985

Fix one bug in constrained generation of initial trees. bug was due to creation on 1 taxon tree with height 0.

7 lines of code changed in 2 files:

• src/dr/evomodel/coalescent: CoalescentSimulator.java (+3 -2)
• src/dr/evomodelxml/coalescent: CoalescentSimulatorParser.java (+4 -2)

jheled 2011-04-07 09:23 Rev.: 3927

Correctly handle calibration on root

14 lines of code changed in 1 file:

• src/dr/evomodel/speciation: BirthDeathGernhard08Model.java (+14 -3)

jheled 2011-03-24 13:20 Rev.: 3898

validation for RPN expressions

57 lines of code changed in 6 files:

• src/dr/inference/model: RPNcalculatorStatistic.java (+7 -2), RPNexpressionCalculator.java (new)
• src/dr/inferencexml/model: RPNcalculatorStatisticParser.java (new)

jheled 2010-11-21 17:51 Rev.: 3729

Add chs, log and exp tp RPN calculator
Add Tree height statistic parser tp .properties

Special calibration cases use RPN expression.

170 lines of code changed in 7 files:

• src/dr/app/beast: development_parsers.properties (+4 -1)
• src/dr/evomodel/speciation: BirthDeathGernhard08Model.java (+37 -21), SpeciationLikelihood.java (+31 -15), SpeciationModel.java (+2 -5), UltrametricSpeciationModel.java (+31 -16)
• src/dr/evomodelxml/speciation: SpeciationLikelihoodParser.java (+40 -12)
• src/dr/inference/model: RPNexpressionCalculator.java (+25 -1)

jheled 2010-11-12 15:59 Rev.: 3713

First implementation of correct calibration density for one monophyletic clade inside a Yule tree.

Allow an "explicit" correction via pre computed coefficients, used when putting additional constraints on the topology

43 lines of code changed in 5 files:

• src/dr/evomodel/speciation: BirthDeathGernhard08Model.java (+22 -10), SpeciationLikelihood.java (+4 -2), SpeciationModel.java (+1 -1), UltrametricSpeciationModel.java (+9 -5)
• src/dr/evomodelxml/speciation: SpeciationLikelihoodParser.java (+7 -1)

jheled 2010-11-11 22:26 Rev.: 3704

First implementation of correct calibration density for one monophyletic clade inside a Yule tree.

The internal interface it a little clunky since the concept does not fit well with the current classes implementing the various speciation priors.

The XML interface is via an additional 'calibration' element inside
the speciationLikelihood. The element contains the taxa and a distribution for the root of the taxa. For a single taxon list, the distribution is for the parent of the taxon, which has no other constraints.

<speciationLikelihood id="speciationlike">
<model>
<yuleModel idref="yule"/>
</model>
<speciesTree>
<treeModel idref="treeModel"/>
</speciesTree>

<calibration>
<exponentialDistributionModel>
<mean>
<parameter id="mean" value="1"/>
</mean>
</exponentialDistributionModel>
<taxa>
<taxon idref="tip1"/>
<taxon idref="tip2"/>
</taxa>
</calibration>
</speciationLikelihood>

158 lines of code changed in 10 files:

• src/dr/evolution/tree: NodeRef.java (new), Tree.java (+25)
• src/dr/evomodel/speciation: BirthDeathGernhard08Model.java (+33 -8), SpeciationLikelihood.java (+20), SpeciationModel.java (+18), UltrametricSpeciationModel.java (+33)
• src/dr/evomodelxml/speciation: SpeciationLikelihoodParser.java (+27 -6), YuleModelParser.java (+1 -2)

jheled 2010-11-11 22:16 Rev.: 3703

automatic intelliJ minor syntax fixes

8 lines of code changed in 6 files:

• src/dr/app/tools: TimeSlicer.java (+1 -1)
• src/dr/evolution/tree: TreeShape.java (+5 -5)
• src/dr/evomodel/operators: NNI.java (new)
• src/dr/inference/trace: TraceCorrelation.java (+1 -1)

jheled 2010-11-09 11:52 Rev.: 3701

Allows any number of tempratures in command line

92 lines of code changed in 2 files:

• src/dr/app/beast: BeastMC3.java (+13 -1)
• src/dr/app/util: Arguments.java (+79 -44)

jheled 2010-10-25 19:15 Rev.: 3669

Give a more intuitive error message

5 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+5 -3)

jheled 2010-10-25 19:13 Rev.: 3668

Give a sane message when no files are given (since files with a non-approved extension, even if explicitly given on the command line, are silently filtered out)

5 lines of code changed in 1 file:

• src/dr/app/tools: TreeLogAnalyser.java (+5)

jheled 2010-09-27 17:57 Rev.: 3580

Now that times() is used to print values in log, change implementation to return only the externally visible ones.

2 lines of code changed in 2 files:

• src/dr/evomodel/coalescent: VDdemographicFunction.java (+2 -2)

jheled 2010-09-24 13:14 Rev.: 3570

Catch errors which lead to beast infinite loop or failure in parsers. more detailed error messages.

18 lines of code changed in 8 files:

• src/dr/evomodelxml/operators: ExchangeOperatorParser.java (+3), SubtreeSlideOperatorParser.java (new)
• src/dr/inference/distribution: MixedDistributionLikelihood.java (new)
• src/dr/inferencexml/distribution: MixedDistributionLikelihoodParser.java (new)
• src/dr/inferencexml/operators: UniformOperatorParser.java (+4)

jheled 2010-08-25 21:58 Rev.: 3446

Ignore nonesense ESS on constant values. integer ESS values in panel.

11 lines of code changed in 1 file:

• src/dr/app/tracer/application: TracerFrame.java (+11 -3)

jheled 2010-06-06 20:49 Rev.: 3232

Add an option to dump all demographics to a file

33 lines of code changed in 4 files:

• src/dr/evomodel/coalescent: EBSPAnalysis.java (new)
• src/dr/evomodelxml/coalescent: EBSPAnalysisParser.java (+12 -1)

jheled 2010-06-06 20:48 Rev.: 3231

Remove annoying debug print

3 lines of code changed in 1 file:

• src/dr/inference/trace: TraceFactory.java (+3 -3)

jheled 2010-06-02 07:05 Rev.: 3212

Allow multiple moves

16 lines of code changed in 1 file:

• src/dr/inference/operators: UniformIntegerOperator.java (+16 -6)

(423 more)