-
msuchard
2009-12-30 11:47
#55
Rev.: 2723
-
99 lines of code changed in 1 file:
-
src/dr/evomodel/continuous:
AbstractMultivariateTraitLikelihood.java (+99 -3)
-
msuchard
2009-12-30 05:22
#54
Rev.: 2722
-
16 lines of code changed in 1 file:
-
src/dr/evomodel/continuous:
AbstractMultivariateTraitLikelihood.java (+16 -4)
-
msuchard
2009-12-24 06:17
#53
Rev.: 2721
-
114 lines of code changed in 2 files:
-
src/dr/evomodel/continuous:
AbstractMultivariateTraitLikelihood.java (+2 -4)
-
src/dr/geo:
Polygon2D.java (+112 -70)
-
alexander.alekseyenko
2009-12-24 05:42
#52
Rev.: 2720
-
133 lines of code changed in 3 files:
-
src/dr/inference/mcmc:
MarginalLikelihoodEstimator.java (+20 -4)
-
src/dr/inference/operators:
CombinedOperatorSchedule.java (+97)
-
src/dr/inference/trace:
PathSamplingAnalysis.java (+16 -4)
-
philippe.lemey@gmail.com
2009-12-24 04:15
#51
Rev.: 2719
-
68 lines of code changed in 1 file:
-
src/dr/geo:
Polygon2D.java (+68 -9)
-
Sibon.Li@gmail.com
2009-12-23 17:11
#50
Rev.: 2718
-
4 lines of code changed in 2 files:
-
src/dr/app/beast:
BeastParser.java (+2)
-
src/dr/evomodel/branchratemodel:
MixtureModelBranchRates.java (+2)
-
Sibon.Li@gmail.com
2009-12-23 17:10
#49
Rev.: 2717
-
85 lines of code changed in 2 files:
-
src/dr/evomodel/branchratemodel:
DiscretizedBranchRates.java (+68 -5)
-
src/dr/evomodelxml:
DiscretizedBranchRatesParser.java (new 17)
-
Sibon.Li@gmail.com
2009-12-23 11:17
#48
Rev.: 2716
-
20 lines of code changed in 2 files:
-
src/dr/evomodel/tree:
TreeLogger.java (+10 -11)
-
src/dr/evomodelxml:
TreeLoggerParser.java (new 10)
-
msuchard
2009-12-23 05:06
#47
Rev.: 2715
-
21 lines of code changed in 1 file:
-
src/dr/evomodel/continuous:
AbstractMultivariateTraitLikelihood.java (+21 -14)
-
msuchard
2009-12-22 12:15
#46
Rev.: 2714
-
27 lines of code changed in 2 files:
-
src/dr/evomodel/branchratemodel:
ArbitraryBranchRates.java (+21 -11)
-
src/dr/inferencexml:
PriorParsers.java (new 6)
-
dong.w.xie
2009-12-22 11:35
#45
Rev.: 2713
-
18 lines of code changed in 5 files:
-
src/dr/app/tools:
BeastParserDoc.java (+9 -8)
-
src/dr/xml:
AbstractXMLObjectParser.java (-1),
WikiDocumentationHandler.java (new),
XMLDocumentationHandler.java (+5)
-
Sibon.Li@gmail.com
2009-12-22 10:53
#44
Rev.: 2711
-
13 lines of code changed in 3 files:
-
src/dr/app/tools:
MixtureModelLogAnalyser.java (+10 -65),
TreeLengthFinder.java (new)
-
Sibon.Li@gmail.com
2009-12-22 10:41
#43
Rev.: 2710
-
346 lines of code changed in 1 file:
-
src/dr/app/tools:
MixtureModelLogAnalyser.java (+346)
-
msuchard
2009-12-22 05:20
#42
Rev.: 2709
-
53 lines of code changed in 1 file:
-
src/dr/evomodel/branchratemodel:
ArbitraryBranchRates.java (+53 -12)
-
rambaut
2009-12-19 04:29
#41
Rev.: 2708
-
18 lines of code changed in 4 files:
-
src/dr/app/coalgen:
CoalGenApp.java (+1 -1)
-
src/dr/app/tools:
NodeStateAnalyser.java (new)
-
src/dr/evomodel/tree:
TreeLengthStatistic.java (+1 -1)
-
dong.w.xie
2009-12-18 10:02
#40
Rev.: 2707
-
33 lines of code changed in 1 file:
-
src/dr/app/tracer/analysis:
BayesianSkylineDialog.java (+33 -8)
-
msuchard
2009-12-18 06:09
#39
Rev.: 2705
-
430 lines of code changed in 12 files:
-
src/dr/app/beast:
development_parsers.properties (+3 -3)
-
src/dr/evomodel/continuous:
VonMisesFisherDiffusionModel.java (+54 -44)
-
src/dr/geo/distributions:
FisherBinghamKentDistribution.java (+7 -2),
HyperSphereDistribution.java (+67 -1),
VonMisesDistribution.java (new),
VonMisesFisherDistribution.java (+62 -3)
-
src/dr/geo/math:
Space.java (new 12)
-
src/dr/inference/model:
FiniteSetParameter.java (+113)
-
src/dr/math/distributions:
AsymptoticBifractionalDiffusionDensity.java (+89)
-
rambaut
2009-12-18 03:53
#38
Rev.: 2704
-
411 lines of code changed in 9 files:
-
src/dr/app/coalgen:
CoalGenApp.java (+1 -1),
CoalGenData.java (+24 -5),
CoalGenFrame.java (+32 -26),
CoalGenMenuFactory.java (new),
DataPanel.java (+107 -281),
InputsPanel.java (+139),
ModelPanel.java (+18 -26),
SimulationsPanel.java (+87)
-
dong.w.xie
2009-12-17 13:00
#37
Rev.: 2703
-
1 lines of code changed in 1 file:
-
src/dr/app/beauti:
BeautiApp.java (+1 -1)
-
dong.w.xie
2009-12-16 15:55
#36
Rev.: 2701
-
66 lines of code changed in 4 files:
-
release/common/doc:
BEASTParserLibrary (new)
-
src/dr/app/tools:
BeastParserDoc.java (+24 -16)
-
src/dr/xml:
WikiDocumentationHandler.java (+38 -4),
XMLDocumentationHandler.java (+4 -4)
-
dong.w.xie
2009-12-16 10:01
#35
Rev.: 2699
-
6 lines of code changed in 2 files:
-
src/dr/app/beauti/priorsPanel:
PriorDialog.java (+1 -1),
RealNumberField.java (+5 -1)
-
msuchard
2009-12-15 07:46
#34
Rev.: 2698
-
0 lines of code changed in 1 file:
-
src/dr/geo/distributions:
HyperSphereDistribution.java (-2)
-
msuchard
2009-12-15 06:40
#33
Rev.: 2697
-
590 lines of code changed in 23 files:
-
src/dr/app/tools:
DiscreteRatePriorGenerator.java (+1 -1),
TimeSlicer.java (+1 -1)
-
src/dr/evolution/continuous:
ContinuousTraitLikelihood.java (new),
SphericalPolarCoordinates.java (del),
Vector3D.java (del)
-
src/dr/evomodel/continuous:
GreatCircleDiffusionModel.java (+1 -1),
TreeDispersionStatistic.java (+1 -1),
VonMisesFisherDiffusionModel.java (+1 -1)
-
src/dr/evomodel/newtreelikelihood:
GeneralLikelihoodCore.java (-1),
OTFPCGeneralLikelihoodCore.java (-2)
-
src/dr/evoxml:
PolarCoordinatesParser.java (new)
-
src/dr/geo:
GreatCircleDistances.java (+1 -1)
-
src/dr/geo/distributions:
FisherBinghamKentDistribution.java (+32),
HyperSphereDistribution.java (+49),
VonMisesDistribution.java (+23),
VonMisesFisherDistribution.java (+23)
-
src/dr/geo/math:
SphericalPolarCoordinates.java (new 252),
Vector3D.java (new 203)
-
msuchard
2009-12-14 11:45
#32
Rev.: 2696
-
104 lines of code changed in 2 files:
-
src/dr/evolution/continuous:
SphericalPolarCoordinates.java (new 5)
-
src/dr/evomodel/continuous:
VonMisesFisherDiffusionModel.java (+99)
-
rambaut
2009-12-12 03:50
#31
Rev.: 2694
-
3 lines of code changed in 1 file:
-
src/dr/evomodel/tree:
NodeHeightsStatistic.java (+3 -3)
-
rambaut
2009-12-12 02:14
#30
Rev.: 2693
-
2 lines of code changed in 2 files:
-
src/dr/app/beast:
BeastParser.java (+2 -1),
release_parsers.properties (-5)
-
rambaut
2009-12-12 02:12
#29
Rev.: 2692
-
171 lines of code changed in 6 files:
-
src/dr/app/beast:
BeastParser.java (+3 -2),
release_parsers.properties (+5)
-
src/dr/evomodel/tree:
NodeHeightsStatistic.java (+146)
-
src/test/dr/evomodel/operators:
OperatorAssert.java (+11 -13)
-
src/test/dr/evomodel/speciation:
RLYModelTest.java (+3 -4),
YuleModelTest.java (+3 -4)
-
rambaut
2009-12-12 01:47
#28
Rev.: 2691
-
175 lines of code changed in 7 files:
-
lib:
jam.jar (changed)
-
src/dr/evolution/coalescent:
PiecewiseConstantPopulation.java (+13),
PiecewiseLinearPopulation.java (+9)
-
src/dr/evomodel/tree:
TreeLengthStatistic.java (+114),
TreelengthStatistic.java (del)
-
msuchard
2009-12-11 04:25
#27
Rev.: 2690
-
36 lines of code changed in 1 file:
-
src/dr/evomodel/continuous:
StochasticDifferentialEquationModel.java (new 36)
-
dong.w.xie
2009-12-10 16:25
#26
Rev.: 2689
-
5 lines of code changed in 1 file:
-
src/dr/util:
ErrorLogHandler.java (+5 -1)
-
dong.w.xie
2009-12-10 16:15
#25
Rev.: 2688
-
1 lines of code changed in 1 file:
-
src/dr/geo:
GreatCircleDistances.java (+1 -1)
-
dong.w.xie
2009-12-10 16:03
#24
-
44 lines of code changed in 3 files:
-
src/dr/app/tools:
BeastParserDoc.java (+22 -22)
-
src/dr/evolution/util:
Taxa.java (+21 -4)
-
src/dr/evomodelxml:
BirthDeathModelParser.java (+1 -1)
-
dong.w.xie
2009-12-10 15:57
#23
Rev.: 2683
-
43 lines of code changed in 3 files:
-
src/dr/xml:
WikiDocumentationHandler.java (+4 -1),
XMLDocumentationHandler.java (+32 -6),
XMLParser.java (+7 -5)
-
dong.w.xie
2009-12-10 15:49
#22
Rev.: 2682
-
15 lines of code changed in 3 files:
-
src/dr/app/beauti/generator:
LogGenerator.java (+4 -4)
-
src/dr/app/beauti/mcmcpanel:
MCMCPanel.java (+7 -6)
-
src/dr/app/beauti/options:
STARBEASTOptions.java (+4 -2)
-
dong.w.xie
2009-12-10 15:29
#21
Rev.: 2681
-
65 lines of code changed in 7 files:
-
src/dr/app/beast:
BeastDialog.java (+9),
BeastMC3.java (+5 -5),
BeastMain.java (+25 -29),
BeastParser.java (+17 -12),
BeastRemote.java (new),
BeastVersion.java (+1 -1)
-
dong.w.xie
2009-12-10 15:16
#20
Rev.: 2680
-
7 lines of code changed in 1 file:
-
dong.w.xie
2009-12-10 13:55
#19
Rev.: 2679
-
52 lines of code changed in 2 files:
-
src/dr/app/beast:
development_parsers.properties (+25 -27),
release_parsers.properties (+27 -1)
-
dong.w.xie
2009-12-10 13:44
#18
Rev.: 2678
-
1407 lines of code changed in 45 files:
-
src/dr/app/beauti:
BeautiFrame.java (+13 -1)
-
src/dr/app/beauti/datapanel:
DataPanel.java (+14)
-
src/dr/app/beauti/enumTypes:
PriorType.java (+69),
SequenceErrorType.java (changed)
-
src/dr/app/beauti/generator:
AlignmentGenerator.java (+128),
BeastGenerator.java (+31 -200),
InitialTreeGenerator.java (+25 -40),
LogGenerator.java (+7 -6),
OperatorsGenerator.java (+1 -1),
STARBEASTGenerator.java (+2 -2),
SubstitutionModelGenerator.java (+33 -18),
TMRCAStatisticsGenerator.java (+87),
TreeLikelihoodGenerator.java (+32 -31),
TreePriorGenerator.java (+5 -4)
-
src/dr/app/beauti/mcmcpanel:
MCMCPanel.java (+59 -13)
-
src/dr/app/beauti/operatorspanel:
OperatorsPanel.java (+11 -5)
-
src/dr/app/beauti/options:
BeautiOptions.java (+44 -6),
ClockModelOptions.java (+1 -1),
ModelOptions.java (+4 -3),
Parameter.java (+23 -19),
PartitionClockModelTreeModelLink.java (+4 -2),
PartitionData.java (+15 -5),
PartitionSubstitutionModel.java (+109 -52),
PartitionTreeModel.java (-3),
PartitionTreePrior.java (+50 -40),
PriorOptions.java (+21 -22),
STARBEASTOptions.java (+6 -8)
-
src/dr/app/beauti/priorsPanel:
DefaultPriorDialog.java (+71),
PriorDialog.java (+41 -14),
PriorOptionsPanel.java (+2 -1),
PriorTableModel.java (+4 -2),
PriorsPanel.java (+42 -14),
RealNumberField.java (+242),
SpecialNumberPanel.java (+93)
-
src/dr/app/beauti/siteModelsPanel:
PartitionModelPanel.java (+37 -21)
-
src/dr/app/beauti/taxonsetspanel:
TaxaPanel.java (+57 -32)
-
src/dr/app/beauti/tipdatepanel:
GuessDatesDialog.java (changed),
TipDatesPanel.java (+7 -15)
-
src/dr/app/beauti/treespanel:
PartitionTreePriorPanel.java (+5 -4)
-
src/dr/app/beauti/util:
BEAUTiImporter.java (+2 -2),
CommandLineBeauti.java (+1 -4)
-
src/dr/app/oldbeauti:
BeastGenerator.java (+2 -2),
BeautiOptions.java (+4 -4)
-
src/test/dr/beauti:
BeautiTesterConfig.java (+2 -2)
-
src/test/dr/evomodel/operators:
ImportanceSubtreeSwapTest.java (new 1)
-
dong.w.xie
2009-12-10 13:34
#17
Rev.: 2675
-
15901 lines of code changed in 69 files:
-
doc/Virus Practical Tex:
Practical_Viruses.pdf (del)
-
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)
-
examples/Data:
Dengue4.env.aminoacid.nex (new 48),
Dengue4.env.nex (new 54),
Primates.nex (+14),
Shankarappa.Patient9.nex (new 259),
anolis.nex (new 37)
-
examples/beauti1.5/starBEAST:
YuleMultiLoci.xml (new 1640),
YuleSingleLocus.xml (new 414),
birthDeathMultiLoci.xml (new 1891),
brithDeathSingleLocus.xml (new 426),
g10.xml (-2036),
g11.xml (-1891),
x10.xml (-414),
x11.xml (-426)
-
examples/beauti1.5/treePrior+clockModel:
BayesianSkyline+unccorelatedExp.xml (new 320),
GMRFBayesianSkyride+strict .xml (new 282),
Yule+unccorelatedExp.xml (new 313),
birthDeath+unccorelatedLn.xml (new 327),
constant+uncorrelatedExp.xml (new 309),
expansionDoubling+strict.xml.xml (new 306),
exponentialDoubling+strict.xml (new 281),
extendedBayesianSkyline+uncorrelatedLn.xml (new 402),
logisticDoubling+uncorrelatedLn.xml (new 347)
-
examples/treePriors:
testCataclysmCoalescent.xml (new)
-
release/common:
README.txt (+7 -5),
VERSION HISTORY.txt (+91 -2)
-
release/common/examples:
Darwins-finches.nex (del),
Dengue4.env.nex (del),
Gopher Data (del),
Primates.nex (del),
Shankarappa.Patient9.nex (del),
anolis.nex (del),
arg-ecoli.xml (del)
-
release/common/examples/Data:
Darwins-finches.nex (new 46),
Dengue4.env.nex (new 54),
Primates.nex (new 14),
Shankarappa.Patient9.nex (new 259),
anolis.nex (new 37)
-
release/common/examples/Data/Gopher Data:
26.nex (new 63),
29.nex (new 64),
47.nex (new 67),
53.nex (new 63),
59.nex (new 64),
64.nex (new 64),
72.nex (new 64)
-
release/common/examples/starBEAST:
YuleMultiLoci.xml (new 1640),
YuleSingleLocus.xml (new 414),
birthDeathMultiLoci.xml (new 1891),
brithDeathSingleLocus.xml (new 426)
-
release/common/examples/treePrior+clockModel:
BayesianSkyline+unccorelatedExp.xml (new 320),
GMRFBayesianSkyride+strict .xml (new 282),
Yule+unccorelatedExp.xml (new 313),
birthDeath+unccorelatedLn.xml (new 327),
constant+uncorrelatedExp.xml (new 309),
expansionDoubling+strict.xml.xml (new 306),
exponentialDoubling+strict.xml (new 281),
extendedBayesianSkyline+uncorrelatedLn.xml (new 402),
logisticDoubling+uncorrelatedLn.xml (new 347)
-
release/common/examples/treePriors:
testCataclysmCoalescent.xml (new 8)
-
msuchard
2009-12-10 05:36
#16
Rev.: 2673
-
257 lines of code changed in 10 files:
-
examples:
testMarkovJumps.xml (new 11)
-
src/dr/app/beagle/evomodel/parsers:
MarkovJumpsTreeLikelihoodParser.java (+58 -14)
-
src/dr/app/beagle/evomodel/substmodel:
MarkovJumpsSubstitutionModel.java (+74 -14)
-
src/dr/app/beagle/evomodel/treelikelihood:
AncestralStateBeagleTreeLikelihood.java (+6 -4),
MarkovJumpsBeagleTreeLikelihood.java (+49 -11)
-
src/dr/app/beast:
BeastMain.java (+1 -1)
-
src/dr/evomodel/continuous:
AbstractMultivariateTraitLikelihood.java (+4 -4)
-
src/dr/evomodel/treelikelihood:
AncestralStateTreeLikelihood.java (+10 -9)
-
src/dr/inference/markovjumps:
MarkovJumpsCore.java (+8 -5),
MarkovJumpsType.java (+36)
-
rambaut
2009-12-05 05:33
#15
Rev.: 2656
-
17 lines of code changed in 1 file:
-
src/dr/inference/markovchain:
MarkovChain.java (+17 -14)
-
Sibon.Li@gmail.com
2009-12-04 16:58
#14
Rev.: 2655
-
691 lines of code changed in 4 files:
-
src/dr/evomodel/branchratemodel:
MixtureModelBranchRates.java (+224),
RandomDiscretizedBranchRates.java (+249)
-
src/dr/evomodelxml:
MixtureModelBranchRatesParser.java (new 124),
RandomDiscretizedBranchRatesParser.java (new 94)
-
msuchard
2009-12-04 06:42
#13
Rev.: 2653
-
303 lines of code changed in 1 file:
-
src/dr/math:
MittagLefflerFunction.java (new 303)
-
msuchard
2009-12-03 07:14
#12
Rev.: 2651
-
111 lines of code changed in 2 files:
-
src/dr/evomodel/continuous:
BifractionalDiffusionModel.java (+56)
-
src/dr/evoxml:
BifractionalDiffusionModelParser.java (+55)
-
Sibon.Li@gmail.com
2009-12-02 16:57
#11
Rev.: 2650
-
2 lines of code changed in 2 files:
-
src/dr/app/tools:
NormaliseMeanTreeRate.java (new)
-
Sibon.Li@gmail.com
2009-12-02 16:56
#10
Rev.: 2649
-
4 lines of code changed in 1 file:
-
src/dr/evomodel/tree:
TreeParameterModel.java (+4 -4)
-
Sibon.Li@gmail.com
2009-12-02 16:49
#9
Rev.: 2648
-
1 lines of code changed in 1 file:
-
src/dr/inference/distribution:
LogNormalDistributionModel.java (+1 -1)
-
dong.w.xie
2009-12-02 13:16
#8
Rev.: 2646
-
29 lines of code changed in 2 files:
-
src/dr/app/beast:
development_parsers.properties (+29 -1),
release_parsers.properties (-28)
-
dong.w.xie
2009-12-02 12:59
#7
Rev.: 2643
-
3 lines of code changed in 2 files:
-
src/dr/app/beast:
development_parsers.properties (+3),
release_parsers.properties (-1)
-
rambaut
2009-12-02 00:07
#6
Rev.: 2642
-
5 lines of code changed in 4 files:
-
build.xml (+1)
-
lib:
figtreepanel.jar (changed)
-
src/dr/app/tools:
TemporalRooting.java (new 4)
-
dong.w.xie
2009-12-01 14:07
#5
Rev.: 2641
-
1 lines of code changed in 1 file:
-
src/dr/app/beast:
BeastMain.java (+1 -3)
-
rambaut
2009-12-01 10:37
#4
Rev.: 2639
-
0 lines of code changed in 1 file:
-
lib:
beagle.jar (changed)
-
rambaut
2009-12-01 09:57
#3
Rev.: 2638
-
2 lines of code changed in 1 file:
-
src/dr/app/phylogeography/spread/layerspanel:
LayersPanel.java (+2 -2)
-
rambaut
2009-12-01 08:55
#2
Rev.: 2637
-
55 lines of code changed in 3 files:
-
build_tracer.xml (+11 -5)
-
src/dr/app/phylogeography/spread/layerspanel:
LayersPanel.java (+43 -43)
-
src/dr/app/tracer/application:
TracerFrame.java (+1 -1)
-
rambaut
2009-12-01 03:37
#1
Rev.: 2636
-
1220 lines of code changed in 19 files:
-
build_pathogen.xml (+1 -1),
build_tracer.xml (+116)
-
src/dr/app/gui:
FileDrop.java (+939),
MultiLineTableCellContent.java (+16),
MultiLineTableCellRenderer.java (+37)
-
src/dr/app/phylogeography/builder:
Builder.java (+1 -1)
-
src/dr/app/phylogeography/gui:
MultiLineTableCellContent.java (del),
MultiLineTableCellRenderer.java (del)
-
src/dr/app/phylogeography/spread:
InputFile.java (+1 -1)
-
src/dr/app/phylogeography/spread/inputpanel:
InputPanel.java (+1 -1)
-
src/dr/app/phylogeography/spread/layerspanel:
LayersPanel.java (+1 -1)
-
src/dr/app/tracer/analysis:
GMRFSkyrideDialog.java (+4 -4)
-
src/dr/app/tracer/application:
TracerApp.java (+2 -2),
TracerFrame.java (+36 -6)
-
src/dr/app/tracer/traces:
CombinedTraces.java (+3 -1),
JTraceChart.java (+42 -48),
RawTracePanel.java (+7 -10)
-
src/dr/gui/chart:
Axis.java (+1 -1),
ChartRuntimeException.java (new 12)