February 2008 Commit Log

Commit Logs

jheled 2008-02-25 16:00 #10 Rev.: 724

nee 1994 birth death model

0 lines of code changed in 1 file:

jheled 2008-02-25 15:56 #9 Rev.: 723

Remove unused call, which used an incorrect cast.

2 lines of code changed in 1 file:

jheled 2008-02-25 15:55 #8 Rev.: 722

add nee 1994 birth/death model. fix likelihood calculation by adding the ignored "tree probability".

90 lines of code changed in 6 files:

src/dr/app/beast: BeastParser.java (+3 -1)
src/dr/app/beastdev: BeastParser.java (+3 -1)
src/dr/evomodel/speciation: MrBayesDefaultModel.java (new 55), SpeciationLikelihood.java (+2 -15), SpeciationModel.java (+26 -4), YuleModel.java (+1 -1)

rambaut 2008-02-23 00:34 #7 Rev.: 714

Minor tweaks

631 lines of code changed in 4 files:

build_development.xml (del)
src/dr/app/beauti: ModelPanel.java (+345 -345), OperatorsPanel.java (+2 -2), PriorsPanel.java (+284 -284)

jheled 2008-02-05 08:27 #6 Rev.: 693

small fix for column name when percentiles are used

2 lines of code changed in 1 file:

jheled 2008-02-04 12:00 #5 Rev.: 690

beauti support for extended skyline

249 lines of code changed in 7 files:

src/dr/app/beauti: BeastGenerator.java (+153 -18), BeautiOptions.java (+46 -10), PriorsPanel.java (+35 -26)
src/dr/evomodel/coalescent: VariableDemographicModel.java (+6 -6)
src/dr/evomodel/coalescent/operators: SampleNonActiveGibbsOperator.java (+5 -4)
src/dr/inference/operators: ScaleOperator.java (+3 -2), SimpleMCMCOperator.java (+1 -1)

rambaut 2008-02-01 23:06 #4 Rev.: 683

Updated JEBL jar file in /lib

0 lines of code changed in 1 file:

rambaut 2008-02-01 02:26 #3 Rev.: 682

Fixed issue 42

3 lines of code changed in 1 file:

rambaut 2008-02-01 02:01 #2 Rev.: 678

Fixed issue 39

10 lines of code changed in 3 files:

rambaut 2008-02-01 01:40 #1 Rev.: 677

Lower limit of 1.0E-8 on GTR parameters and kappa to stop them going to zero under a Jeffrey's prior.

43 lines of code changed in 1 file:

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