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Sibon.Li@gmail.com 2012-11-15 11:24 Rev.: 5228

Updated InstantiableTracerApp to include an option to load a System exitable instance of Tracer

54 lines of code changed in 2 files:

• src/dr/app/tracer/application: InstantiableTracerApp.java (+54 -13)

Sibon.Li@gmail.com 2012-10-25 15:23 Rev.: 5207

RandomDiscretizedBranchRates has been renamed to the more meaningful ContinuousBranchRates. RandomDiscretizedBranchRatesParser has been kept and throws an error in the unlikely case that someone actually has been using this implementation.

390 lines of code changed in 8 files:

• src/dr/app/beast: release_parsers.properties (+11 -1)
• src/dr/app/tracer/application: InstantiableTracerApp.java (+34 -1)
• src/dr/evomodel/branchratemodel: ContinuousBranchRates.java (new 244), RandomDiscretizedBranchRates.java (del)
• src/dr/evomodelxml/branchratemodel: ContinuousBranchRatesParser.java (new 94), DiscretizedBranchRatesParser.java (new), RandomDiscretizedBranchRatesParser.java (new 7)

Sibon.Li@gmail.com 2012-09-18 19:14 Rev.: 5170

Changes to MarkovChainDelegate to allow it better access and privileges to MarkovChain

2 lines of code changed in 4 files:

• src/dr/inference/markovchain: MarkovChainDelegate.java (+1 -1)
• src/dr/inference/mcmc: MCMC.java (new)

Sibon.Li@gmail.com 2012-09-18 17:42 Rev.: 5169

Added InstantiableTracerApp, which allows a threaded call of Tracer (that won't terminate the JVM)

153 lines of code changed in 1 file:

• src/dr/app/tracer/application: InstantiableTracerApp.java (+153)

Sibon.Li@gmail.com 2010-03-01 15:31 Rev.: 2994

Fixed the parameterisation of the burnin to that of the LogAnalyser (instead of the TreeAnnotator)

1 lines of code changed in 1 file:

• src/dr/app/tools: MixtureModelLogAnalyser.java (+1 -4)

Sibon.Li@gmail.com 2010-02-23 14:55 Rev.: 2961

Fixed my last commit

16 lines of code changed in 4 files:

• src/dr/app/beast: BeastVersion.java (+4 -4)
• src/dr/evomodelxml: MixtureModelBranchRatesParser.java (del)
• src/dr/evomodelxml/branchratemodel: MixtureModelBranchRatesParser.java (new)

Sibon.Li@gmail.com 2010-02-23 14:38 Rev.: 2960

Modified MixtureModelBranchRates to not have to take in quantiles

156 lines of code changed in 2 files:

• src/dr/evomodel/branchratemodel: MixtureModelBranchRates.java (+32 -3)
• src/dr/evomodelxml: MixtureModelBranchRatesParser.java (new 124)

Sibon.Li@gmail.com 2009-12-23 17:11 Rev.: 2718

Added MixtureModelBranchRates

4 lines of code changed in 2 files:

• src/dr/app/beast: BeastParser.java (+2)
• src/dr/evomodel/branchratemodel: MixtureModelBranchRates.java (+2)

Sibon.Li@gmail.com 2009-12-23 17:10 Rev.: 2717

Added work in progress to discretizedBranchRates to allow for normalising of the mean branch rate (does not yet work properly but does not effect existing operations)

85 lines of code changed in 2 files:

• src/dr/evomodel/branchratemodel: DiscretizedBranchRates.java (+68 -5)
• src/dr/evomodelxml: DiscretizedBranchRatesParser.java (new 17)

Sibon.Li@gmail.com 2009-12-23 11:17 Rev.: 2716

Removed normalised mean rate function of TreeLogger

20 lines of code changed in 2 files:

• src/dr/evomodel/tree: TreeLogger.java (+10 -11)
• src/dr/evomodelxml: TreeLoggerParser.java (new 10)

Sibon.Li@gmail.com 2009-12-22 10:53 Rev.: 2711

Tidied up some code

13 lines of code changed in 3 files:

• src/dr/app/tools: MixtureModelLogAnalyser.java (+10 -65), TreeLengthFinder.java (new)

Sibon.Li@gmail.com 2009-12-22 10:41 Rev.: 2710

Created tool MixtureModelLogAnalyser which can parses discrete variables in the log trace

346 lines of code changed in 1 file:

• src/dr/app/tools: MixtureModelLogAnalyser.java (+346)

Sibon.Li@gmail.com 2009-12-04 16:58 Rev.: 2655

Uploaded two new relaxed clock implementations/models, RandomDiscretizedBranchRates and MixtureModelBranchRates.

691 lines of code changed in 4 files:

• src/dr/evomodel/branchratemodel: MixtureModelBranchRates.java (+224), RandomDiscretizedBranchRates.java (+249)
• src/dr/evomodelxml: MixtureModelBranchRatesParser.java (new 124), RandomDiscretizedBranchRatesParser.java (new 94)

Sibon.Li@gmail.com 2009-12-02 16:57 Rev.: 2650

Modified text output from NormaliseMeanTreeRate

2 lines of code changed in 2 files:

• src/dr/app/tools: NormaliseMeanTreeRate.java (new)

Sibon.Li@gmail.com 2009-12-02 16:56 Rev.: 2649

Fixed bug with TreeParameterModel where double should've been used instead of int

4 lines of code changed in 1 file:

• src/dr/evomodel/tree: TreeParameterModel.java (+4 -4)

Sibon.Li@gmail.com 2009-12-02 16:49 Rev.: 2648

LogNormalDistribution isMeanInRealSpace is actually defaulted to false

1 lines of code changed in 1 file:

• src/dr/inference/distribution: LogNormalDistributionModel.java (+1 -1)

Sibon.Li@gmail.com 2009-10-19 13:32 Rev.: 2435

Changed example file for Auto-correlated relaxed clock to incorporate new changes to input format in ACLikelihood

13 lines of code changed in 1 file:

• examples: testAutocorrelatedRelaxedClock.xml (new 13)

Sibon.Li@gmail.com 2009-10-16 13:16 Rev.: 2426

Added amino acid version of Dengue4.env.nex

0 lines of code changed in 1 file:

• examples: Dengue4.env.aminoacid.nex (new)

Sibon.Li@gmail.com 2009-10-14 13:31 Rev.: 2391

Fixed up an error message in InverseGaussianDistributionModel

1 lines of code changed in 1 file:

• src/dr/inference/distribution: InverseGaussianDistributionModel.java (+1 -1)

Sibon.Li@gmail.com 2009-10-07 17:25 Rev.: 2360

InverseGaussian distribution can now take in either a shape or stdev parameter

102 lines of code changed in 1 file:

• src/dr/inference/distribution: InverseGaussianDistributionModel.java (+102 -22)

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