Directory src/test/dr/evomodel/substmodel/

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msuchard 2013-01-16 10:50 Rev.: 5327

Eigendecomposition check uses anonymous subclass that turns off condition number evaluation.

8 lines of code changed in 2 files:

• src/test/dr/evomodel/substmodel: SpecificEigendecompositionTest.java (+8 -6)

mdhall272@gmail.com 2013-01-15 23:01 Rev.: 5325

Added some other matrices that don't work.

47 lines of code changed in 1 file:

• src/test/dr/evomodel/substmodel: SpecificEigendecompositionTest.java (+47 -9)

mdhall272@gmail.com 2013-01-15 06:05 Rev.: 5322

Cleaning up.

60 lines of code changed in 2 files:

• src/test/dr/evomodel/substmodel: EigendecompositionTest.java (+60 -30)

msuchard 2012-12-21 05:22 Rev.: 5291

Increased max iterations and largest allowable condition number for complex diagonalizable substitution models; may change inference in BSSVS models.

101 lines of code changed in 1 file:

• src/test/dr/evomodel/substmodel: SpecificEigendecompositionTest.java (+101)

mdhall272@gmail.com 2012-12-21 02:07 Rev.: 5290

changed to take a user-specified matrix

157 lines of code changed in 1 file:

• src/test/dr/evomodel/substmodel: EigendecompositionTest.java (+157 -84)

msuchard 2012-12-19 16:06 Rev.: 5283

Preliminary test unit for failure of eigen decompositions

249 lines of code changed in 1 file:

• src/test/dr/evomodel/substmodel: EigendecompositionTest.java (+249)

msuchard 2012-01-10 02:55 Rev.: 4572

Adding a CnCs counting class

60 lines of code changed in 2 files:

• src/test/dr/evomodel/substmodel: CodonPartitionedRobustCountingTest.java (new)

dong.w.xie 2011-11-24 11:00 Rev.: 4481

trunk:solve Issue 457: BEAST should raise an error if binary dataType set but data is not binary, and Issue 312: BEAST continues to run (inappropriately) when sequence contains invalid character

5 lines of code changed in 2 files:

• src/test/dr/evomodel/substmodel: TimeIrreversibleTest.java (new)

dong.w.xie 2011-09-15 14:37 Rev.: 4314

trunk: add Junit test for GF81

139 lines of code changed in 1 file:

• src/test/dr/evomodel/substmodel: GeneralF81Test.java (new 139)

sibon.li 2011-06-21 12:46 Rev.: 4053

Transferring my changes from branch 1.6 to trunk:

Changes to LogNormalDistributionModel to allow for the stdev value to also not
be in log space (r3774)
Changes to UncorrelatedRelaxedClockTest due to changes in
LogNormalDistributionModel in r3774 (r3775)
Minor change in MixtureModelBranchRates to fix an issue caused by changes in
revision 3735 (r3773)
Bug fix for AncestralSequenceAnnotator plus added a window to select
input/output files (r3819)
Fixed spelling for GeneralSubstitutionModelTest (r3833)
Fixed a RuntimeException for AncestralStateTreeLikelihood (r3957)

178 lines of code changed in 2 files:

• src/test/dr/evomodel/substmodel: GeneralSubsitutionModelTest.java (del), GeneralSubstitutionModelTest.java (new 178)

akaruiws 2011-04-01 09:47 Rev.: 3914

Correcting according to changes made to the models.

3 lines of code changed in 2 files:

• src/test/dr/evomodel/substmodel: MsatSamplingTreeLikelihoodTest.java (+3 -3)

akaruiws 2011-04-01 01:16 Rev.: 3911

Tidy up MsatBMA related things.

1 lines of code changed in 2 files:

• src/test/dr/evomodel/substmodel: TwoPhaseModelTest.java (new)

akaruiws 2011-02-17 15:37 Rev.: 3806

BMA for nucleotide substition models and gamma site model.

96 lines of code changed in 2 files:

• src/test/dr/evomodel/substmodel: testNtdBMA.java (new)

akaruiws 2011-02-15 17:04 Rev.: 3802

GTR examples added.

59 lines of code changed in 1 file:

• src/test/dr/evomodel/substmodel: testNtdBMA.java (+59 -12)

akaruiws 2011-02-15 16:17 Rev.: 3801

TN93 example added.

11 lines of code changed in 1 file:

• src/test/dr/evomodel/substmodel: testNtdBMA.java (+11 -9)

akaruiws 2011-02-15 15:29 Rev.: 3800

Some quick JUnit tests for NtdBMA model to check whether there are any major problems. More useful tests yet to come.

227 lines of code changed in 1 file:

• src/test/dr/evomodel/substmodel: testNtdBMA.java (+227)

dong.w.xie 2010-09-24 10:38 Rev.: 3568

Trunk: active a JUnit test

269 lines of code changed in 1 file:

• src/test/dr/evomodel/substmodel: TimeIrreversibleTest.java (+269)

alexei.drummond 2010-07-28 15:44 Rev.: 3333

updated Birth-death serial sampling model

5 lines of code changed in 2 files:

• src/test/dr/evomodel/substmodel: TwoStateCovarionModelTest.java (+5 -3)

akaruiws 2010-07-01 17:32 Rev.: 3298

Gibbs sampling for a single msat ancestral state.

19 lines of code changed in 5 files:

• src/test/dr/evomodel/substmodel: AsymQuadTest.java (+6), LinearBiasTest.java (new), TwoPhaseModelTest.java (+6 -1)

akaruiws 2010-06-18 18:45 Rev.: 3275

Importance sampling for the msat ancestral states.

21 lines of code changed in 3 files:

• src/test/dr/evomodel/substmodel: AsymQuadTest.java (+8 -1), LinearBiasTest.java (+7), TwoPhaseModelTest.java (+6 -1)

akaruiws 2010-06-06 22:12 Rev.: 3233

Misc changes to classes for msat likelihood calculation.

212 lines of code changed in 1 file:

• src/test/dr/evomodel/substmodel: MsatSamplingTreeLikelihoodTest.java (+212)

msuchard 2010-05-21 13:19 Rev.: 3178

Can now simulate sequences under a branch-specific substitution model; for example, different dN/dS per branch.

79 lines of code changed in 3 files:

• src/test/dr/evomodel/substmodel: CompleteHistorySimulatorTest.java (+10 -3), VariableBranchCompleteHistorySimulatorTest.java (new 69)

msuchard 2010-05-17 11:00 Rev.: 3170

Preparing MarkovJumps to compute null distributions for tests of selection using just nucleotide models (fast, fast, fast)

244 lines of code changed in 2 files:

• src/test/dr/evomodel/substmodel: MarkovJumpsSubstitutionModelTest.java (new 186), ProductChainFrequencyModelTest.java (new 58)

msuchard 2010-03-25 13:02 Rev.: 3071

Can now simulate (and report) the complete history of any model in BEAST, most importantly codon models (with branch rate variation) and report the true number of synonymous and nonsynonymous mutations in a synthetic dataset.

158 lines of code changed in 1 file:

• src/test/dr/evomodel/substmodel: CompleteHistorySimulatorTest.java (+158)

msuchard 2010-03-25 06:23 Rev.: 3070

Further work for RobustCounting

115 lines of code changed in 3 files:

• src/test/dr/evomodel/substmodel: ProductChainSubstitutionModelTest.java (+2 -16), StateHistoryTest.java (new 113)

msuchard 2010-03-01 09:27 Rev.: 2991

Robust counting is working (as far as I can tell) and returns expected numbers of syn and non-syn changes on a tree, using just nucleotide models

70 lines of code changed in 1 file:

• src/test/dr/evomodel/substmodel: ProductChainSubstitutionModelTest.java (+70 -7)

msuchard 2010-02-27 09:30 Rev.: 2990

(1) More testing of robust counting; (2) more work on a citation framework

206 lines of code changed in 2 files:

• src/test/dr/evomodel/substmodel: CodonPartitionedRobustCountingTest.java (+205 -29), ProductChainSubstitutionModelTest.java (+1 -46)

msuchard 2010-02-26 15:46 Rev.: 2988

Added JUnitTest for counting synonymous jumps; also refactored a function in making codon models to avoid duplicating code

67 lines of code changed in 1 file:

• src/test/dr/evomodel/substmodel: CodonPartitionedRobustCountingTest.java (+67)

msuchard 2010-02-25 16:20 Rev.: 2983

Made some comments about handling missing trait values for the integrateTraitLikelihood

44 lines of code changed in 1 file:

• src/test/dr/evomodel/substmodel: ProductChainSubstitutionModelTest.java (+44 -33)

msuchard 2010-02-25 15:04 Rev.: 2980

Product chain test is now working for 2-state cross 2-state model; next will write a test for nucleotide cross nucleotide cross nucleotide

43 lines of code changed in 1 file:

• src/test/dr/evomodel/substmodel: ProductChainSubstitutionModelTest.java (+43 -9)

msuchard 2010-02-25 09:43 Rev.: 2977

Still working on product chain models and robust counting

77 lines of code changed in 1 file:

• src/test/dr/evomodel/substmodel: ProductChainSubstitutionModelTest.java (+77 -5)

msuchard 2010-02-24 03:53 Rev.: 2965

Intermediate steps in implementing robust counting of S and N using nucleotide models

61 lines of code changed in 1 file:

• src/test/dr/evomodel/substmodel: ProductChainSubstitutionModelTest.java (+61)

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

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

4 lines of code changed in 1 file:

• src/test/dr/evomodel/substmodel: GeneralSubsitutionModelTest.java (new 4)

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

Trunk refactoring: make subst parsers more organized.

1 lines of code changed in 1 file:

• src/test/dr/evomodel/substmodel: GeneralSubsitutionModelTest.java (+1 -1)

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

Trunk refactoring: site model (split parsers).

2 lines of code changed in 1 file:

• src/test/dr/evomodel/substmodel: GeneralSubsitutionModelTest.java (+2 -1)

dong.w.xie 2010-02-17 12:00 Rev.: 2929

Trunk refactoring: big part of substitution model (split parsers).

4 lines of code changed in 1 file:

• src/test/dr/evomodel/substmodel: GeneralSubsitutionModelTest.java (+4 -3)

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/substmodel: GeneralSubsitutionModelTest.java (+1 -1)

dong.w.xie 2010-02-05 15:15 Rev.: 2887

Trunk: enable general sub model test, and correct the rate1 expectation in xml.

175 lines of code changed in 1 file:

• src/test/dr/evomodel/substmodel: GeneralSubsitutionModelTest.java (+175)

dong.w.xie 2010-02-04 09:15 Rev.: 2878

Trunk: update test.

3 lines of code changed in 1 file:

• src/test/dr/evomodel/substmodel: TwoStateCovarionModelTest.java (+3 -3)

dong.w.xie 2010-02-03 09:57 Rev.: 2874

Trunk: incomplete correction of 2state coarion model, and leave to Alexei to complete.

21 lines of code changed in 1 file:

• src/test/dr/evomodel/substmodel: TwoStateCovarionModelTest.java (+21 -4)

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