Directory examples/

Total Files:
1
Deleted Files:
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Lines of Code:
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Lines of Code

examples/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
Totals 279 (100.0%) 37749 (100.0%) 135.3
bloomquist 6 (2.2%) 10512 (27.8%) 1752.0
rambaut 51 (18.3%) 10511 (27.8%) 206.0
msuchard 55 (19.7%) 6649 (17.6%) 120.8
alexei.drummond 48 (17.2%) 3636 (9.6%) 75.7
jheled 23 (8.2%) 3473 (9.2%) 151.0
alexander.alekseyenko 13 (4.7%) 1196 (3.2%) 92.0
Michael.DefoinPLatel 4 (1.4%) 816 (2.2%) 204.0
dong.w.xie 74 (26.5%) 414 (1.1%) 5.5
Sibon.Li@gmail.com 3 (1.1%) 399 (1.1%) 133.0
higgs.ml 1 (0.4%) 143 (0.4%) 143.0
akaruiws 1 (0.4%) 0 (0.0%) 0.0

Most Recent Commits

dong.w.xie 2012-02-15 09:36 Rev.: 4694

trunk: add xml test batch file

5 lines of code changed in 1 file:

  • examples: test.sh (new 5)
dong.w.xie 2010-08-26 16:11

Trunk: refactory xml examples

0 lines of code changed in 61 files:

  • examples: Mdor phygeo ages1.xml (del), Msat (del), arg-ecoli.xml (del), arg-lepto.xml (del), arg-rokas.xml (del), benchmark.xml (del), benchmark2.xml (del), demoCodonHistorySimulator.xml (del), new_benchmark.xml (del), testAlignmentStatistics.xml (del), testAncestralReconstruction.xml (del), testAscertainment.xml (del), testAutocorrelatedRelaxedClock.xml (del), testBSP.xml (del), testBinaryDollo.xml (del), testCTMCMap.xml (del), testCodonLikelihood.xml (del), testComparativeMethod.xml (del), testCompleteHistorySimulator.xml (del), testConjugateTraitLikelihood.xml (del), testCovarionHKY.xml (del), testDiscreteMapDiffusion.xml (del), testGeneralSubstitutionModel.xml (del), testIA.xml (del), testIBDweights.xml (del), testIntegratedTraitLikelihood.xml (del), testLewisMk.xml (del), testLikelihood.xml (del), testLinearRegression.xml (del), testLocalClock.xml (del), testLognormalPrior.xml (del), testMC3.xml (del), testMCMC.xml (del), testML.xml (del), testMLCalculator.xml (del), testMSSD.xml (del), testMVOU.xml (del), testMarkovJumps.xml (del), testMissingIntegratedTraitLikelihood.xml (del), testMixedModel.xml (del), testMultiThreading.xml (del), testMultivariateComparativeMethod.xml (del), testNewLikelihood.xml (del), testNormalModelGibbs.xml (del), testOTFPCLikelihood.xml (del), testPMD.xml (del), testPathSampling.xml (del), testPopTreeModel.xml (del), testPosteriorIBD.xml (del), testRandomLocalClock.xml (del), testRestrictedAncestralReconstruction.xml (del), testRobustCounting.xml (del), testSequenceSimulator.xml (del), testSimplePathSampling.xml (del), testStrictClock.xml (del), testTransmission.xml (del), testTransmissionStatistic.xml (del), testTreePathSampling.xml (del), testUncorrelatedRelaxedClock.xml (del), testUniformizedMarkovJumps.xml (del), testYuleOneSite.xml (del)
rambaut 2010-08-25 23:32 Rev.: 3447

Implemented some microtiming in CompoundLikelihood. This is turned on by a static constant in this class so won't be compiled unless switched on. The results can be obtained by dumping the CompoundLikelihood into a <report> element:

<report>
<posterior idref="posterior"/>
</report>

This will break down the total number of evalations, the total amount of time and the time per eval for every prior and likelihood. This will be useful for considering parallelization and threading options.

The switch (CompoundLikelihood.EVALUATION_TIMERS) is on at present as I don't believe it will have any performance implications but I will be checking this.

3 lines of code changed in 1 file:

  • examples: benchmark2.xml (new 3)
rambaut 2010-08-20 18:49 Rev.: 3415

Added a benchmark2.xml file with 62 complete mitochondrial genomes of carnivores. Gives >5000 unique site patterns.

580 lines of code changed in 1 file:

  • examples: benchmark2.xml (+580)
msuchard 2010-07-13 09:12 Rev.: 3303

Can independently specify root distribution from CTMC stationary distribution

255 lines of code changed in 1 file:

  • examples: testRestrictedAncestralReconstruction.xml (new 255)
msuchard 2010-06-17 10:45 Rev.: 3273

Critical fix: branch rates now print out in tree log under new TreeTrait framework. Also starting to remove duplicated code from classes needing to output different combinations of TreeTrait summaries

2 lines of code changed in 1 file:

  • examples: testRobustCounting.xml (new 2)
akaruiws 2010-06-06 22:12 Rev.: 3233

Misc changes to classes for msat likelihood calculation.

0 lines of code changed in 1 file:

  • examples: Msat (new)
msuchard 2010-05-29 08:37 Rev.: 3197

Two goals acheived. (1) RobustCounting now provides per site counts to a log file and (2) example of using a helper class to log traits from a TraitProvider, will remove substantial duplicated code from CPRC and MJBTL

7 lines of code changed in 1 file:

  • examples: testRobustCounting.xml (+7 -1)
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.

15 lines of code changed in 1 file:

  • examples: testCompleteHistorySimulator.xml (new 15)
msuchard 2010-04-24 06:58 Rev.: 3132

MarkovJumpsBeagleTreeLikelihood now supports all CTMC that can be uniformized (I believe this is all finite-state models).

152 lines of code changed in 1 file:

  • examples: testUniformizedMarkovJumps.xml (new 152)
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.

273 lines of code changed in 2 files:

  • examples: demoCodonHistorySimulator.xml (new 88), testCompleteHistorySimulator.xml (+185)
msuchard 2010-03-04 14:52 Rev.: 3020

Added FullyConjugateMultivariateTraitLikelihood; the Gibbs sampler to come next

148 lines of code changed in 3 files:

  • examples: testConjugateTraitLikelihood.xml (new 124), testIntegratedTraitLikelihood.xml (new 10), testMissingIntegratedTraitLikelihood.xml (new 14)
msuchard 2010-03-01 12:24 Rev.: 2992

Updating robust counting output

4 lines of code changed in 1 file:

  • examples: testRobustCounting.xml (+4 -1)
msuchard 2010-02-26 08:31 Rev.: 2986

Sampling missing values appears to also be working

14 lines of code changed in 1 file:

  • examples: testMissingIntegratedTraitLikelihood.xml (+14 -14)
msuchard 2010-02-26 08:20 Rev.: 2985

Missing data in IntegratedMultivariateTraitLikelihood appears to be working; use "NA" in taxon trait.

115 lines of code changed in 1 file:

  • examples: testMissingIntegratedTraitLikelihood.xml (+115)
msuchard 2010-02-24 03:53 Rev.: 2965

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

443 lines of code changed in 1 file:

  • examples: testRobustCounting.xml (+443)
rambaut 2010-02-10 03:57 Rev.: 2906

Resolved an arbitrary contraction of a constant name.

592 lines of code changed in 1 file:

  • examples: testLikelihood.xml (new 592)
dong.w.xie 2010-02-09 09:55 Rev.: 2899

Trunk: delete duplicate xml.

0 lines of code changed in 1 file:

  • examples: testRelaxedClock.xml (del)
dong.w.xie 2010-02-05 15:15 Rev.: 2887

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

185 lines of code changed in 1 file:

  • examples: testGeneralSubstitutionModel.xml (new 185)
alexander.alekseyenko 2010-02-02 11:31 Rev.: 2866

Started on Population Tree Approximation models.

39 lines of code changed in 1 file:

  • examples: testPopTreeModel.xml (new 39)
msuchard 2010-01-26 18:16 Rev.: 2840

Bug fixes for integrated Brownian diffusion.

32 lines of code changed in 1 file:

  • examples: testIntegratedTraitLikelihood.xml (+32 -10)
msuchard 2010-01-25 20:11 Rev.: 2837

Integrated Brownian diffusion now supports full conditional sampling of internal nodes.

93 lines of code changed in 1 file:

  • examples: testIntegratedTraitLikelihood.xml (+93)
msuchard 2010-01-09 05:42 Rev.: 2788

Added a very simple path sampling example involving a phylogenetic problem (2-taxon tree, testing \kappa = 10 vs \kappa random)

0 lines of code changed in 1 file:

  • examples: testTreePathSampling.xml (new)
msuchard 2010-01-06 17:15 Rev.: 2748

Added a very simple path sampling example and some minor tweaks to GMRF skyrides and the TraitGibbsOperator

251 lines of code changed in 1 file:

  • examples: testSimplePathSampling.xml (new 251)
dong.w.xie 2010-01-05 09:07 Rev.: 2727

Trunk: Re-adding xml file deleted in r2675

224 lines of code changed in 1 file:

  • examples: testYuleOneSite.xml (new 224)
msuchard 2010-01-01 03:47 Rev.: 2725

Re-adding version of file that shows how to use Markov rewards

11 lines of code changed in 1 file:

  • examples: testMarkovJumps.xml (new 11)
msuchard 2010-01-01 03:30 Rev.: 2724

Re-adding two files deleted in r2673 (why?)

164 lines of code changed in 2 files:

  • examples: testAlignmentStatistics.xml (new 23), testMarkovJumps.xml (+141)
dong.w.xie 2009-12-10 13:34 Rev.: 2675

Trunk: start merge from branch 1.5 in

0 lines of code changed in 9 files:

  • examples: Dengue4.env.aminoacid.nex (del), Dengue4.env.nex (del), Primates.nex (del), Shankarappa.Patient9.nex (del), anolis.nex (del), testAlignmentStatistics.xml (del), testMarkovJumps.xml (del), testOTFPCLikelihood.xml (new), testYuleOneSite.xml (del)
msuchard 2009-12-10 05:36 Rev.: 2673

MarkovJumps now supports Markov reward processes. Also a typo fix in BeastMain and some unnecessary casting in AMTL.

11 lines of code changed in 1 file:

  • examples: testMarkovJumps.xml (new 11)
msuchard 2009-11-30 08:34 Rev.: 2626

MarkovJumps now processes multiple register matrices at a time

21 lines of code changed in 1 file:

  • examples: testMarkovJumps.xml (+21 -2)
msuchard 2009-11-27 08:43 Rev.: 2620

Smashing bugs in MarkovJumps

29 lines of code changed in 1 file:

  • examples: testMarkovJumps.xml (+29 -6)
msuchard 2009-11-25 17:43 Rev.: 2607

Fixed MarkovJumps to work when mutation rate is specified in siteModel

19 lines of code changed in 1 file:

  • examples: testMarkovJumps.xml (+19 -22)
msuchard 2009-11-25 15:17 Rev.: 2602

Small test file for MarkovJumps

102 lines of code changed in 1 file:

  • examples: testMarkovJumps.xml (+102)
msuchard 2009-11-24 11:08 Rev.: 2590

Tested alignment statistics; appear fine.

23 lines of code changed in 1 file:

  • examples: testAlignmentStatistics.xml (new 23)
alexei.drummond 2009-11-09 14:17 Rev.: 2519

224 lines of code changed in 1 file:

  • examples: testYuleOneSite.xml (new 224)
alexander.alekseyenko 2009-10-23 02:57 Rev.: 2449

added parsers for Lewis' Mk model with totaly ordered/unordered/custom ordered states.

31 lines of code changed in 1 file:

  • examples: testLewisMk.xml (new 31)
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)
msuchard 2009-10-06 06:04 Rev.: 2349

Fixes to CachedDistributionLikelihood to work with MultivariateDistributionLikelihood. Tweaks to eigendecomposition routines, in case of invalid diagonalization

1 lines of code changed in 1 file:

  • examples: new_benchmark.xml (new 1)
rambaut 2009-08-20 08:02 Rev.: 2110

New benchmark XML

371 lines of code changed in 1 file:

  • examples: new_benchmark.xml (+371)

(90 more)

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