Directory src/dr/evomodelxml/branchratemodel/

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rambaut 2013-04-18 23:15 Rev.: 5598

DiscreteTraitBranchRateModel parser tweaks.

26 lines of code changed in 2 files:

• src/dr/evomodelxml/branchratemodel: DiscreteTraitBranchRateModelParser.java (new)

rambaut 2013-04-18 22:35 Rev.: 5597

DiscreteTraitBranchRateModel parser tweaks.

2 lines of code changed in 1 file:

• src/dr/evomodelxml/branchratemodel: DiscreteTraitBranchRateModelParser.java (+2 -2)

rambaut 2013-03-14 00:00 Rev.: 5482

Created an 'AttributeBranchRateModel' which exposes an attribute embedded in a tree as a branch rate model.

81 lines of code changed in 1 file:

• src/dr/evomodelxml/branchratemodel: AttributeBranchRateModelParser.java (new 81)

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.

101 lines of code changed in 4 files:

• src/dr/evomodelxml/branchratemodel: ContinuousBranchRatesParser.java (new 94), DiscretizedBranchRatesParser.java (new), RandomDiscretizedBranchRatesParser.java (new 7)

msuchard 2012-09-12 10:00 Rev.: 5152

Added skew-normal distribution model

32 lines of code changed in 2 files:

• src/dr/evomodelxml/branchratemodel: ArbitraryBranchRatesParser.java (+32 -1)

rambaut 2012-02-18 06:23 Rev.: 4707

Debugging DTBRM

1 lines of code changed in 1 file:

• src/dr/evomodelxml/branchratemodel: DiscreteTraitBranchRateModelParser.java (+1 -1)

rambaut 2011-11-11 23:58 Rev.: 4415

DiscreteTraitBranchRateModel with Markov rewards

21 lines of code changed in 1 file:

• src/dr/evomodelxml/branchratemodel: DiscreteTraitBranchRateModelParser.java (+21 -12)

rambaut 2011-04-28 04:27 Rev.: 3964

3 lines of code changed in 1 file:

• src/dr/evomodelxml/branchratemodel: ArbitraryBranchRatesParser.java (+3 -2)

msuchard 2011-03-21 07:36 Rev.: 3884

Parameter dimension check for arbitrary branch rates

7 lines of code changed in 1 file:

• src/dr/evomodelxml/branchratemodel: ArbitraryBranchRatesParser.java (+7 -1)

dong.w.xie 2010-07-08 11:08 Rev.: 3300

TRUNK: solve Issue 325: processValues[] in DiscreteTraitBranchRateModel should be the size of number of states NOT number of rates

11 lines of code changed in 1 file:

• src/dr/evomodelxml/branchratemodel: DiscreteTraitBranchRateModelParser.java (+11 -2)

msuchard 2010-06-14 14:48 Rev.: 3265

DiscreteTraitBranchRateModel now works again for ancestral state reconstructions. Something is still wrong with AncestralStateBeagleTreeLikelihood however.

1 lines of code changed in 1 file:

• src/dr/evomodelxml/branchratemodel: DiscreteTraitBranchRateModelParser.java (+1 -1)

rambaut 2010-06-13 23:31 Rev.: 3262

Added a 'backbone' local clock to LocalClockModel (sorry it took so long Philippe).

23 lines of code changed in 2 files:

• src/dr/evomodelxml/branchratemodel: LocalClockModelParser.java (+23 -1)

rambaut 2010-06-13 03:05 Rev.: 3256

Additional work on DiscreteTraitBranchRateModel - adding an indicator parameter to provide link between state and rate.

1 lines of code changed in 1 file:

• src/dr/evomodelxml/branchratemodel: DiscreteTraitBranchRateModelParser.java (+1 -1)

rambaut 2010-06-12 22:52 Rev.: 3255

Trying a reparameterization of DTBRM

10 lines of code changed in 1 file:

• src/dr/evomodelxml/branchratemodel: DiscreteTraitBranchRateModelParser.java (+10 -3)

rambaut 2010-06-12 22:09 Rev.: 3254

Additional work on DiscreteTraitBranchRateModel - adding an indicator parameter to provide link between state and rate.

8 lines of code changed in 1 file:

• src/dr/evomodelxml/branchratemodel: DiscreteTraitBranchRateModelParser.java (+8 -1)

rambaut 2010-06-07 23:59 Rev.: 3236

Normalized the naming of a few classes and added a note in the MCMC parser to say if the fullEvaluation has been turned off.

86 lines of code changed in 3 files:

• src/dr/evomodelxml/branchratemodel: ContinuousTraitBranchRateModelParser.java (+1 -1), DiscreteTraitBranchRateModelParser.java (+85)

jheled 2010-06-02 07:04 Rev.: 3211

code police

1 lines of code changed in 1 file:

• src/dr/evomodelxml/branchratemodel: DiscretizedBranchRatesParser.java (+1 -1)

rambaut 2010-06-02 00:12 Rev.: 3207

This update does a number of things. 1) TreeLoggerParser and DemographicLoggerParser were in dr.inferencexml which breaks the dependency rules as they link to things in dr.evomodel. These are now moved to dr.evomodelxml. 2) A dr.evolution.tree.TreeTrait interface is created which is a general purpose interface for access to traits on nodes/branches. BranchAttributeProvider and NodeAttributeProvider will be replaced by this interface in the next update. 3) All BranchRateModels now have a common abstract base class AbstractBranchRateModel to implement their common features (these now implement TreeTrait to provide rates).

75 lines of code changed in 2 files:

• src/dr/evomodelxml/branchratemodel: ContinuousTraitBranchRateModelParser.java (+75), TraitBranchRateModelParser.java (del)

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

Fixed my last commit

12 lines of code changed in 2 files:

• src/dr/evomodelxml/branchratemodel: MixtureModelBranchRatesParser.java (new)

dong.w.xie 2010-02-22 10:42 Rev.: 2954

Trunk refactoring: organize tree and treelikelihood parsers.

1 lines of code changed in 2 files:

• src/dr/evomodelxml/branchratemodel: RateEpochBranchRateModelParser.java (+1 -1)

rambaut 2010-02-20 02:02 Rev.: 2949

Local clocks on the stem lineages only.

10 lines of code changed in 1 file:

• src/dr/evomodelxml/branchratemodel: LocalClockModelParser.java (+10 -4)

dong.w.xie 2010-02-18 16:36 Rev.: 2941

Trunk refactoring: finish branch rate and clock rate model (split parsers).

253 lines of code changed in 3 files:

• src/dr/evomodelxml/branchratemodel: RandomLocalClockModelParser.java (new 73), RateEpochBranchRateModelParser.java (+130), StrictClockBranchRatesParser.java (new 50)

dong.w.xie 2010-02-18 10:12 Rev.: 2939

Trunk refactoring: branch rate and clock rate model (split parsers).

682 lines of code changed in 8 files:

• src/dr/evomodelxml/branchratemodel: ArbitraryBranchRatesParser.java (+64), CompoundBranchRateModelParser.java (new 63), DiscretizedBranchRatesParser.java (+96), LocalClockModelParser.java (+120), MixtureModelBranchRatesParser.java (+115), RandomDiscretizedBranchRatesParser.java (+94), ScaledTreeLengthRateModelParser.java (new 53), TraitBranchRateModelParser.java (new 77)