Directory src/test/dr/evomodel/treelikelihood/

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rambaut 2011-11-16 05:15 Rev.: 4433

Ported sequence error models to BeagleTreeLikelihood and implemented a variant model that emits tip states rather than tip partials.

2 lines of code changed in 2 files:

• src/test/dr/evomodel/treelikelihood: PMDTestProblem.java (+2 -2)

rambaut 2010-09-02 02:22 Rev.: 3480

Fixed a few issues with SequenceErrorModel. Also added an automatic dimension setting for the popsize parameter in GMRF.

2 lines of code changed in 1 file:

• src/test/dr/evomodel/treelikelihood: PMDTestProblem.java (+2 -2)

msuchard 2010-07-13 15:21 Rev.: 3304

Pacifying Hudson.

5 lines of code changed in 2 files:

• src/test/dr/evomodel/treelikelihood: SequenceLikelihoodTest.java (+5 -5)

msuchard 2010-07-13 02:36 Rev.: 3302

Checking normalization of CTMC likelihood over all possible alignments

244 lines of code changed in 4 files:

• src/test/dr/evomodel/treelikelihood: AscertainmentCorrectedLikelihoodTest.java (new), NormalizedSequenceLikelihoodTest.java (new 108), SequenceLikelihoodTest.java (+135)

msuchard 2010-06-06 04:51 Rev.: 3229

Added an ascertainment correction unit test.

190 lines of code changed in 3 files:

• src/test/dr/evomodel/treelikelihood: AscertainmentCorrectedLikelihoodTest.java (+189), LikelihoodTest.java (new)

rambaut 2010-06-02 22:53 Rev.: 3215

TreeTraits commit number 2. This one is a bit more wide ranging with potential to break things. 1) BranchAttributeProvider and NodeAttributeProvider have been deleted and replaced with a combination of TreeTraits and TreeTraitProviders. Sources implement TreeTraitProvider to say that they can provide information about nodes and branches. A good example of a class which has been generalized is AncestralState (in evomodel.treelikelihood) - this now just takes a TreeTrait and logs the trait for a given MRCA (the trait can be anything at all - whereas previously it took an AncestralStateTreeLikelihood).

3 lines of code changed in 2 files:

• src/test/dr/evomodel/treelikelihood: AncestralStateTreeLikelihoodTest.java (new)

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).

1 lines of code changed in 1 file:

• src/test/dr/evomodel/treelikelihood: AncestralStateTreeLikelihoodTest.java (+1 -1)

dong.w.xie 2010-02-24 16:25 Rev.: 2974

Trunk refactoring: 1st part of Likelihoods (split parsers)..

3 lines of code changed in 1 file:

• src/test/dr/evomodel/treelikelihood: PMDTestProblem.java (+3 -2)

dong.w.xie 2010-02-23 09:35 Rev.: 2959

Trunk refactoring: finish tree likihood model (split parsers)..

6 lines of code changed in 1 file:

• src/test/dr/evomodel/treelikelihood: PMDTestProblem.java (+6 -4)

dong.w.xie 2010-02-19 14:41 Rev.: 2943

Trunk refactoring: finish coalescent (split parsers).

2 lines of code changed in 1 file:

• src/test/dr/evomodel/treelikelihood: PMDTestProblem.java (+2 -1)

dong.w.xie 2010-02-17 16:04 Rev.: 2935

Trunk refactoring: make subst parsers more organized.

3 lines of code changed in 2 files:

• src/test/dr/evomodel/treelikelihood: LikelihoodTest.java (+2 -2), PMDTestProblem.java (+1 -1)

dong.w.xie 2010-02-17 15:45 Rev.: 2934

Trunk refactoring: site model (split parsers).

21 lines of code changed in 2 files:

• src/test/dr/evomodel/treelikelihood: LikelihoodTest.java (+19 -18), PMDTestProblem.java (+2 -1)

dong.w.xie 2010-02-17 12:29 Rev.: 2930

Trunk refactoring: finish substitution model (split parsers).

25 lines of code changed in 1 file:

• src/test/dr/evomodel/treelikelihood: LikelihoodTest.java (+25 -24)

dong.w.xie 2010-02-11 14:24 Rev.: 2911

Trunk: record result for further diagnose.

89 lines of code changed in 1 file:

• src/test/dr/evomodel/treelikelihood: PMDTestProblem.java (+89)

dong.w.xie 2010-02-11 09:16 Rev.: 2910

Trunk: add new test without enable, because it has problem.

231 lines of code changed in 1 file:

• src/test/dr/evomodel/treelikelihood: PMDTestProblem.java (+231)

dong.w.xie 2010-02-10 16:04 Rev.: 2908

Trunk: update tesst.

1 lines of code changed in 1 file:

• src/test/dr/evomodel/treelikelihood: LikelihoodTest.java (+1 -1)

dong.w.xie 2010-01-29 11:12 Rev.: 2857

Trunk: update Junit test for tree likelihood.

192 lines of code changed in 1 file:

• src/test/dr/evomodel/treelikelihood: LikelihoodTest.java (+192)

dong.w.xie 2010-01-29 09:52 Rev.: 2854

Trunk: add and enable new Junit test for tree likelihood.

177 lines of code changed in 1 file:

• src/test/dr/evomodel/treelikelihood: LikelihoodTest.java (+177)

alexei.drummond 2010-01-27 12:34 Rev.: 2846

Marc and Alexei added joint likelihood calculation and test for ancestral state likelihood

103 lines of code changed in 1 file:

• src/test/dr/evomodel/treelikelihood: AncestralStateTreeLikelihoodTest.java (+103)