Directory src/dr/evomodel/arg/coalescent/

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jheled 2009-09-09 08:26 Rev.: 2227

generify and auto intelliJ

12 lines of code changed in 2 files:

• src/dr/evomodel/arg/coalescent: VeryOldCoalescentLikelihood.java (new)

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...

4 lines of code changed in 3 files:

• src/dr/evomodel/arg/coalescent: ARGCoalescentLikelihood.java (+2 -2), VeryOldCoalescentLikelihood.java (+2 -2)

jheled 2009-06-23 07:20 Rev.: 1794

automatic idea changes, change type return type of getChild

7 lines of code changed in 2 files:

• src/dr/evomodel/arg/coalescent: ARGCoalescentLikelihood.java (+4 -4), VeryOldCoalescentLikelihood.java (+3 -3)

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/arg/coalescent: VeryOldCoalescentLikelihood.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.

1 lines of code changed in 1 file:

• src/dr/evomodel/arg/coalescent: VeryOldCoalescentLikelihood.java (+1 -1)

bloomquist 2008-12-20 12:53 Rev.: 1395

Added ancestral restriction to ARGCoalescentLikelihood.

17 lines of code changed in 1 file:

• src/dr/evomodel/arg/coalescent: ARGCoalescentLikelihood.java (+17 -5)

bloomquist 2008-12-13 13:13 Rev.: 1387

Modified some minor ARG Stuff. Added statistic to give total ARG length.

1 lines of code changed in 2 files:

• src/dr/evomodel/arg/coalescent: ARGUniformPrior.java (+1 -2)

bloomquist 2008-12-12 12:17 Rev.: 1385

Small change on where it spits out the warning.

0 lines of code changed in 1 file:

• src/dr/evomodel/arg/coalescent: ARGUniformPrior.java (-1)

bloomquist 2008-12-12 11:57 Rev.: 1384

Modifications to the ARG package.

3 lines of code changed in 1 file:

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

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

Moved ParameterChangeType -> Parameter.ChangeType

1 lines of code changed in 1 file:

• src/dr/evomodel/arg/coalescent: VeryOldCoalescentLikelihood.java (+1 -1)

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

added variable size functionality to Parameter

470 lines of code changed in 1 file:

• src/dr/evomodel/arg/coalescent: VeryOldCoalescentLikelihood.java (+470 -470)

msuchard 2008-08-15 12:42 Rev.: 1135

Added a flat prior over ARG space.

1 lines of code changed in 1 file:

• src/dr/evomodel/arg/coalescent: ARGUniformPrior.java (+1 -1)

msuchard 2008-08-14 11:09 Rev.: 1126

Port of ARG classes into the trunk. There are some very silly repeats of code (namely: TreeModel and ARGModel should inherit from a base class, ARGTreeLogger is almost indentical to TreeLogger, and CompoundParameter should replace ARGCompoundParameter).

1416 lines of code changed in 3 files:

• src/dr/evomodel/arg/coalescent: ARGCoalescentLikelihood.java (+310), ARGUniformPrior.java (+422), VeryOldCoalescentLikelihood.java (+684)