Directory src/dr/evomodel/coalescent/structure/

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alexei.drummond 2009-07-19 14:30 Rev.: 1873

Parameter -> Variable, Act 2 -- this is probably the biggest change made to core BEAST in a few years. So I tagged revision 1870 for convenience. Parameter is now basically obsoleted and should be replaced by DoubleVariable or Variable<Double> where appropriate. We can now also develop some Variable<Integer> and Variable<Boolean> et cetera so should be nice in the future... I have also added a Variable<double[]> for vectors and matrices. See dr.inference.tutorial.Tutorial1 for a first peek at programmable BEAST MCMC...

15 lines of code changed in 8 files:

• src/dr/evomodel/coalescent/structure: ColourSamplerModel.java (+6 -6), ConstantMigrationModel.java (+3 -2), MetaPopulationModel.java (new), StructuredCoalescentLikelihood.java (new)

alexei.drummond 2009-07-13 22:26 Rev.: 1844

Refactoring to remove illegal dependencies. No classes in dr.evolution.* packages should depend on classes in dr.evomodel.* or dr.inference.* or dr.evomodelxml. Also converted dr.evolution.coalescent.IntervalType to enum and minor other tidy ups.

17 lines of code changed in 2 files:

• src/dr/evomodel/coalescent/structure: MetaPopulationModel.java (+8 -7), StructuredCoalescentLikelihood.java (+9 -6)

jheled 2009-06-25 06:55 Rev.: 1802

more automatic intelliJ

6 lines of code changed in 2 files:

• src/dr/evomodel/coalescent/structure: ColourSamplerModel.java (+4 -4), ConstantMigrationModel.java (+2 -2)

jheled 2009-04-20 09:10 Rev.: 1607

Continued Marc's refactorization. I wonder what other shared functionality we can pull off in there.

0 lines of code changed in 1 file:

• src/dr/evomodel/coalescent/structure: StructuredCoalescentLikelihood.java (-23)

jheled 2009-04-19 08:35 Rev.: 1598

add a nethod for getting a meaningfull name of a likelihood. more classes may benefit from overriding the default.

4 lines of code changed in 1 file:

• src/dr/evomodel/coalescent/structure: StructuredCoalescentLikelihood.java (+4 -4)

alexei.drummond 2008-11-27 21:21 Rev.: 1340

Moved ParameterChangeType -> Parameter.ChangeType

8 lines of code changed in 4 files:

• src/dr/evomodel/coalescent/structure: ColourSamplerModel.java (+1 -1), ConstantMigrationModel.java (+1 -2), MetaPopulationModel.java (+5 -2), StructuredCoalescentLikelihood.java (+1 -1)

alexei.drummond 2008-11-27 13:08 Rev.: 1337

added variable size functionality to Parameter

161 lines of code changed in 4 files:

• src/dr/evomodel/coalescent/structure: ColourSamplerModel.java (+1 -1), ConstantMigrationModel.java (+18 -15), MetaPopulationModel.java (+105 -100), StructuredCoalescentLikelihood.java (+37 -21)

alexei.drummond 2008-07-10 21:59 Rev.: 987

Tidied up boolean attribute parsing in various classes

51 lines of code changed in 1 file:

• src/dr/evomodel/coalescent/structure: ColourSamplerModel.java (+51 -56)

jheled 2008-06-05 20:25 Rev.: 937

Change method name to something I understand

1 lines of code changed in 1 file:

• src/dr/evomodel/coalescent/structure: ColourSamplerModel.java (+1 -1)

jheled 2007-02-05 11:54 Rev.: 198

partial generification

7 lines of code changed in 1 file:

• src/dr/evomodel/coalescent/structure: MetaPopulationModel.java (+7 -7)

rambaut 2006-12-04 09:38 Rev.: 83

Merged some fixes and improvements I made in the 1.4 branch in to the trunk. This includes the fix for Issue 8 in LogCombiner. Also, I have made some interfaces in the TreeColouring stuff so that other sources of TreeColouring (such as the Transmission history stuff) can provide coloured trees for logging.

13 lines of code changed in 1 file:

• src/dr/evomodel/coalescent/structure: ColourSamplerModel.java (+13 -11)