StatSVN - Directory src/dr/evomodel/beagle/substmodel/

Lines of Code

src/dr/evomodel/beagle/substmodel/ Lines of Code

Developers

Author	Changes	Lines of Code	Lines per Change
Totals	59 (100.0%)	2873 (100.0%)	48.6
rambaut	31 (52.5%)	2406 (83.7%)	77.6
msuchard	11 (18.6%)	271 (9.4%)	24.6
alexei.drummond	16 (27.1%)	189 (6.6%)	11.8
jheled	1 (1.7%)	7 (0.2%)	7.0

Most Recent Commits

rambaut 2009-08-04 03:47 Rev.: 2009

Moving BEAGLE/BEAST out of the main package into dr.app. This will allow us to deploy the jar file separately from BEAST.

0 lines of code changed in 12 files:

src/dr/evomodel/beagle/substmodel: BaseSubstitutionModel.java (del), ColtEigenSystem.java (del), DefaultEigenSystem.java (del), EigenDecomposition.java (del), EigenSystem.java (del), FrequencyModel.java (del), GTR.java (del), GY94CodonModel.java (del), GeneralSubstitutionModel.java (del), HKY.java (del), MarkovModulatedGY94CodonModel.java (del), SubstitutionModel.java (del)

alexei.drummond 2009-07-19 14:30 Rev.: 1873

Parameter -> Variable, Act 2 -- this is probably the biggest change made to core BEAST in a few years. So I tagged revision 1870 for convenience. Parameter is now basically obsoleted and should be replaced by DoubleVariable or Variable<Double> where appropriate. We can now also develop some Variable<Integer> and Variable<Boolean> et cetera so should be nice in the future... I have also added a Variable<double[]> for vectors and matrices. See dr.inference.tutorial.Tutorial1 for a first peek at programmable BEAST MCMC...

187 lines of code changed in 14 files:

src/dr/evomodel/beagle/substmodel: BaseSubstitutionModel.java (new), FrequencyModel.java (new), GTR.java (+12 -12), GY94CodonModel.java (new), GeneralSubstitutionModel.java (+123 -123), HKY.java (new), MarkovModulatedGY94CodonModel.java (new)

jheled 2009-06-23 07:20 Rev.: 1794

automatic idea changes, change type return type of getChild

7 lines of code changed in 1 file:

src/dr/evomodel/beagle/substmodel: GeneralSubstitutionModel.java (+7 -7)

alexei.drummond 2009-06-12 16:21 Rev.: 1775

little things

2 lines of code changed in 2 files:

src/dr/evomodel/beagle/substmodel: SubstitutionModel.java (+2 -4)

rambaut 2009-06-03 09:08 Rev.: 1759

Made some changes to the BEAGLE/BEAST interface to reflect the new BEAGLE API.

67 lines of code changed in 8 files:

src/dr/evomodel/beagle/substmodel: BaseSubstitutionModel.java (+6 -6), ColtEigenSystem.java (+12 -5), DefaultEigenSystem.java (new), EigenDecomposition.java (new), HKY.java (+33 -33)

msuchard 2009-04-14 12:06 Rev.: 1571

Debugging hidden codon models and need to test on larger computer system.

14 lines of code changed in 4 files:

src/dr/evomodel/beagle/substmodel: BaseSubstitutionModel.java (+1 -1), ColtEigenSystem.java (+1 -1), DefaultEigenSystem.java (+1 -1), MarkovModulatedGY94CodonModel.java (+11 -1)

msuchard 2009-04-07 21:19 Rev.: 1536

Added DuplicatedParameter for symmetric rates and assymetric indicators. Added ColtEigenSystem to compare numerical stability in beagle package.

83 lines of code changed in 4 files:

src/dr/evomodel/beagle/substmodel: BaseSubstitutionModel.java (+8 -3), ColtEigenSystem.java (+47), GY94CodonModel.java (+10 -2), MarkovModulatedGY94CodonModel.java (+18 -2)

msuchard 2009-04-06 10:56 Rev.: 1534

Working on path sampling final integration code; some fixes in CompoundSymmetricMatrix to enable MH proposals and retain positive definiteness.

54 lines of code changed in 2 files:

src/dr/evomodel/beagle/substmodel: BaseSubstitutionModel.java (+37 -1), MarkovModulatedGY94CodonModel.java (+17 -19)

msuchard 2009-03-31 12:18 Rev.: 1528

Removed NativeSubstitutionModel (old, defunct code for GPU) and started working on a covarion-like codon models. Here come the 128 and 196 state models!

120 lines of code changed in 1 file:

src/dr/evomodel/beagle/substmodel: MarkovModulatedGY94CodonModel.java (+120)

rambaut 2009-03-25 06:23 Rev.: 1514

Goldman Yang 94 model ported to beagle

381 lines of code changed in 1 file:

src/dr/evomodel/beagle/substmodel: GY94CodonModel.java (+381)

rambaut 2009-03-20 05:08 Rev.: 1504

Towards a working beagle library

187 lines of code changed in 2 files:

src/dr/evomodel/beagle/substmodel: GTR.java (+181), HKY.java (+6 -2)

rambaut 2009-03-19 02:15 Rev.: 1501

I have moved all the new stuff for the 'BEAGLE' library into its own package. I am producing a set of parsers that override the default ones to use the new classes. I envisage that at some point we will want to move to the new SubstModel hierarchy as it is much cleaner. But to avoid breaking anything whilst this develops, I am compartmentalizing them.

1771 lines of code changed in 8 files:

src/dr/evomodel/beagle/substmodel: BaseSubstitutionModel.java (+322), DefaultEigenSystem.java (+668), EigenDecomposition.java (+59), EigenSystem.java (new 38), FrequencyModel.java (+155), GeneralSubstitutionModel.java (+200), HKY.java (+259), SubstitutionModel.java (+70)