January 2011 Commit Log

Number of Commits:

10

Number of Active Developers:

4

mandevsgill 2011-01-30 12:17 #10 Rev.: 3781

Modified precision in smoothing prior for multilocus case.

100 lines of code changed in 1 file:

• src/dr/evomodel/coalescent: GMRFMultilocusSkyrideLikelihood.java (+100 -6)

dong.w.xie 2011-01-27 14:02 #9 Rev.: 3780

Trunk: start a big operation on new Tracer

2 lines of code changed in 2 files:

• src/dr/app/tracer/traces: FilterDialog.java (+2 -1)
• src/dr/inference/trace: TraceDistribution.java (-11)

rambaut 2011-01-26 21:28 #8 Rev.: 3779

A bit of work on the 'TreeSpace' application.

640 lines of code changed in 9 files:

• src/dr/app/treespace: CladePanel.java (new 152), CladeSystem.java (+220), InputFile.java (+7 -3), TimelinePanel.java (del), TreePanel.java (new 149), TreeSpaceDocument.java (new), TreeSpaceFrame.java (+103 -22)

msuchard 2011-01-26 09:54 #7 Rev.: 3778

Fixing bug in ancestral state reconstruction when using ambiguities

19 lines of code changed in 2 files:

• src/dr/app/beagle/evomodel/treelikelihood: AncestralStateBeagleTreeLikelihood.java (+10 -6)
• src/dr/evomodel/treelikelihood: AncestralStateTreeLikelihood.java (+9)

rambaut 2011-01-24 23:18 #6 Rev.: 3777

Some new empirical codon models by Stefan Zoller (ETH Zurich) & Adrian Schneider (U. of Edinburgh). Example files in examples/release/EmpiricalCodonModels

3238 lines of code changed in 29 files:

• examples/release/EmpiricalCodonModels: testECMcodonModel.xml (new 215), testPCMcodonModel.xml (new 206)
• examples/release/EmpiricalCodonModels/codon-data/ecmdata: freqs_k_unrest.csv (new 1), freqs_zs.csv (new 1), inirates.csv (new 1), norates.csv (new 1), rates_k_unrest.csv (new 1), rates_zs.csv (new 1)
• examples/release/EmpiricalCodonModels/codon-data/pcadata: freqs.csv (new 1), means.csv (new 1), pcs.csv (new 100), scales.csv (new 1), startfacs.csv (new 1)
• src/dr/app/beagle/evomodel/parsers: EmpiricalCodonModelParser.java (+165), PCACodonModelParser.java (+154)
• src/dr/app/beagle/evomodel/substmodel: AbstractPCARateMatrix.java (+64), EmpiricalCodonModel.java (+605), EmpiricalRateMatrix.java (+105), PCACodonModel.java (+129), PCARateMatrixMammalia.java (+118)
• src/dr/app/beast: beagle_parsers.properties (+2), release_parsers.properties (+3)
• src/dr/evomodel/substmodel: AbstractPCARateMatrix.java (new 64), EmpiricalCodonModel.java (new 603), EmpiricalCodonRateMatrix.java (new 105), PCACodonModel.java (new 149), PCARateMatrixMammalia.java (new 123)
• src/dr/evomodelxml/substmodel: EmpiricalCodonModelParser.java (new 164), PCACodonModelParser.java (new 154)

rambaut 2011-01-20 12:57 #5 Rev.: 3776

Playing with a new visualization of discrete spatial model.

345 lines of code changed in 1 file:

• src/dr/app/phylogeography/tools: TreeDensityKML.java (+345)

rambaut 2011-01-11 03:21 #4 Rev.: 3772

Added some data to the KML elements to allow for styling by BF etc. Seems to work now.

8 lines of code changed in 1 file:

• src/dr/app/phylogeography/tools: RateIndicatorBF.java (+8 -14)

rambaut 2011-01-11 02:00 #3 Rev.: 3771

Fixes to RateIndicatorBF's output of KML data.

1 lines of code changed in 1 file:

• src/dr/app/phylogeography/tools: RateIndicatorBF.java (+1 -1)

rambaut 2011-01-06 05:04 #2 Rev.: 3770

Added some data to the KML elements to allow for styling by BF etc. Compiles but not yet tested.

263 lines of code changed in 1 file:

• src/dr/app/phylogeography/tools: RateIndicatorBF.java (+263 -162)

msuchard 2011-01-04 08:37 #1 Rev.: 3769

Slightly improved error reporting for multivariate normal parsing

3 lines of code changed in 1 file:

• src/dr/inference/distribution: MultivariateDistributionLikelihood.java (+3 -1)

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