Directory examples/release/

Directory Deleted:
2011-11-11 23:37
Total Files:
0
Deleted Files:
52
Lines of Code:
0

[root]/examples/release
            directory in repo Benchmarks (3 files, 362 lines)
            directory in repo Data (2 files, 51 lines)
            directory in repo EmpiricalCodonModels (2 files, 421 lines)
                directory in repo codon-data (0 files, 0 lines)
                    directory in repo ecmdata (6 files, 6 lines)
                    directory in repo pcadata (5 files, 104 lines)
            directory in repo Phylogeography (0 files, 0 lines)
                directory in repo continuous (3 files, 2252 lines)
            directory in repo calibrations (17 files, 1234 lines)
            directory in repo clockModels (9 files, 2329 lines)
            directory in repo continuousTraits (2 files, 41 lines)
            directory in repo discreteTraits (2 files, 209 lines)
            directory in repo microsatellite (1 files, 1012 lines)
            directory in repo recombination (3 files, 10494 lines)
            Folder removed from repo starBEAST (0 files, 0 lines)
            Folder removed from repo substModels (0 files, 0 lines)
            directory in repo testXML (35 files, 10012 lines)
                directory in repo treePrior+clockModel (8 files, 2540 lines)
            Folder removed from repo treePrior+clockModel (0 files, 0 lines)
            Folder removed from repo treePriors (0 files, 0 lines)

Lines of Code

examples/release/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
Totals 76 (100.0%) 2973 (100.0%) 39.1
dong.w.xie 24 (31.6%) 1932 (65.0%) 80.5
msuchard 4 (5.3%) 768 (25.8%) 192.0
alexander.alekseyenko 4 (5.3%) 235 (7.9%) 58.7
baele.guy@gmail.com 2 (2.6%) 37 (1.2%) 18.5
akaruiws 1 (1.3%) 1 (0.0%) 1.0
rambaut 41 (53.9%) 0 (0.0%) 0.0

Most Recent Commits

rambaut 2011-11-11 23:37 Rev.: 4409

Reorganization of the examples/release folder. Please add/remove anything that will be packaged with the next release.

0 lines of code changed in 1 file:

  • examples/release: treeOpsTest (del)
rambaut 2011-11-11 23:32

Reorganization of the examples/release folder. Please add/remove anything that will be packaged with the next release.

0 lines of code changed in 36 files:

  • examples/release: arg-ecoli.xml (del), arg-lepto.xml (del), arg-rokas.xml (del), testAlignmentStatistics.xml (del), testAncestralReconstruction.xml (del), testAscertainment.xml (del), testAutocorrelatedRelaxedClock.xml (del), testBinaryDollo.xml (del), testCodonLikelihood.xml (del), testComparativeMethod.xml (del), testLatentLiability.xml (del), testLewisMk.xml (del), testLikelihood.xml (del), testLognormalPrior.xml (del), testMC3.xml (del), testMCMC.xml (del), testML.xml (del), testMSSD.xml (del), testMVN.xml (del), testMVOU.xml (del), testMarkovJumps.xml (del), testMissingIntegratedTraitLikelihood.xml (del), testMixedModel.xml (del), testMultiThreading.xml (del), testNormalModelGibbs.xml (del), testPMD.xml (del), testPopTreeModel.xml (del), testPosteriorIBD.xml (del), testRestrictedAncestralReconstruction.xml (del), testSequenceSimulator.xml (del), testSimplePathSampling.xml (del), testStarTreeTest.xml (del), testStarTreeTest2.xml (del), testTransmissionStatistic.xml (del), testTreePathSampling.xml (del), testUniformizedMarkovJumps.xml (del)
msuchard 2011-10-18 08:34 Rev.: 4365

Better way to handle star trees via a derived TreeModel

252 lines of code changed in 1 file:

  • examples/release: testStarTreeTest2.xml (new 252)
msuchard 2011-10-17 03:49 Rev.: 4360

Preliminary star tree implementation as an alternative to the correlated trait models; would function better as a subclass of TreeModel than TreeLikelihood.

258 lines of code changed in 1 file:

  • examples/release: testStarTreeTest.xml (new 258)
msuchard 2011-08-24 12:38 Rev.: 4238

Latent liability model appears to work well.

15 lines of code changed in 1 file:

  • examples/release: testLatentLiability.xml (new 15)
msuchard 2011-08-20 14:02 Rev.: 4222

Implemented Joe Felsenstein's latent liability model with a single new class to BEAST.

243 lines of code changed in 1 file:

  • examples/release: testLatentLiability.xml (+243)
rambaut 2011-08-10 23:59 Rev.: 4180

Test script for multivariate normal prior

0 lines of code changed in 1 file:

  • examples/release: testMVN.xml (new)
dong.w.xie 2011-07-01 14:26 Rev.: 4088

TRUNK: update xmls to compare BEAST 2 results

0 lines of code changed in 1 file:

  • examples/release: testYuleOneSite.xml (del)
baele.guy@gmail.com 2011-06-10 07:15 Rev.: 4022

Added a section to the xml to illustrate usage of the sigmoid integration approach for the beta values when using thermodynamic integration.

26 lines of code changed in 1 file:

  • examples/release: testTreePathSampling.xml (new 26)
baele.guy@gmail.com 2011-06-09 04:27 Rev.: 4018

Adjusted certain output files so that the entire xml file can be performed in a single run (the previous version gave parsing errors). The second marginal likelihood estimator now uses beta quantiles to define the path of the beta values in the thermodynamic integration approach (see Xie et al., 2010 and Fan et al., 2011).

11 lines of code changed in 1 file:

  • examples/release: testTreePathSampling.xml (+11 -11)
akaruiws 2011-02-17 15:37 Rev.: 3806

BMA for nucleotide substition models and gamma site model.

1 lines of code changed in 1 file:

  • examples/release: testMCMC.xml (new 1)
alexander.alekseyenko 2010-09-25 04:58 Rev.: 3571

Started MV Polya Likelihood model

2 lines of code changed in 1 file:

  • examples/release: testMSSD.xml (new 2)
alexander.alekseyenko 2010-09-24 04:20 Rev.: 3567

fix and move a few example files of my making

233 lines of code changed in 3 files:

  • examples/release: testIBDweights.xml (del), testLewisMk.xml (new 25), testMSSD.xml (+208)
rambaut 2010-08-29 01:47 Rev.: 3468

Added a third benchmark file. old_benchmark.xml is the old (trivially small) one. benchmark1.xml is 1400-odd HA1 flu genomes (about 500 patterns) to test big trees with modest amounts of data. benchmark2.xml is 60-odd mitochondrial genomes resulting in >5000 site patterns to test modest trees with lots of data.

0 lines of code changed in 3 files:

  • examples/release: benchmark.xml (del), benchmark2.xml (del), new_benchmark.xml (del)
dong.w.xie 2010-08-27 16:03 Rev.: 3465

Trunk: refactory xml examples

1932 lines of code changed in 10 files:

  • examples/release: testAlignmentStatistics.xml (new 23), testAutocorrelatedRelaxedClock.xml (new 460), testMarkovJumps.xml (new 150), testMissingIntegratedTraitLikelihood.xml (new 115), testPopTreeModel.xml (new 39), testRestrictedAncestralReconstruction.xml (new 255), testSimplePathSampling.xml (new 251), testTreePathSampling.xml (+262), testUniformizedMarkovJumps.xml (new 152), testYuleOneSite.xml (new 225)
dong.w.xie 2010-08-27 13:28 Rev.: 3463

Trunk: refactory xml examples

0 lines of code changed in 11 files:

  • examples/release: arg-ecoli.xml (new), benchmark2.xml (new), testBSP.xml (del), testCovarionHKY.xml (del), testGeneralSubstitutionModel.xml (del), testIA.xml (del), testLocalClock.xml (del), testPathSampling.xml (del), testRandomLocalClock.xml (del), testStrictClock.xml (del), testUncorrelatedRelaxedClock.xml (del)
dong.w.xie 2010-08-27 11:20 Rev.: 3462

Trunk: refactory xml examples

0 lines of code changed in 1 file:

  • examples/release: treeOpsTest (new)
dong.w.xie 2010-08-27 11:14 Rev.: 3461

Trunk: refactory xml examples

0 lines of code changed in 1 file:

  • examples/release: Virus Practical (del)
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