-
dong.w.xie
2011-02-28 13:11
#52
Rev.: 3836
-
31 lines of code changed in 6 files:
-
src/dr/app/beauti:
BeautiFrame.java (-1)
-
src/dr/app/beauti/datapanel:
DataPanel.java (+1 -1)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+15 -1)
-
src/dr/app/beauti/options:
BeautiOptions.java (+1),
TraitData.java (+14 -4)
-
src/dr/app/beauti/traitspanel:
TraitsPanel.java (-6)
-
dong.w.xie
2011-02-28 10:20
#51
Rev.: 3835
-
7 lines of code changed in 2 files:
-
src/dr/app/beauti/datapanel:
DataPanel.java (+5 -3)
-
src/dr/app/beauti/traitspanel:
TraitsPanel.java (+2 -10)
-
dong.w.xie
2011-02-28 10:02
#50
Rev.: 3834
-
3 lines of code changed in 1 file:
-
src/dr/app/beauti:
BeautiFrame.java (+3 -4)
-
rambaut
2011-02-26 05:31
#49
Rev.: 3832
-
190 lines of code changed in 2 files:
-
src/dr/evomodel/continuous:
AntigenicTraitLikelihood.java (+77 -84),
MultidimensionalScalingLikelihood.java (+113 -135)
-
dong.w.xie
2011-02-25 15:20
#48
Rev.: 3831
-
42 lines of code changed in 9 files:
-
src/dr/app/tracer/application:
TracerFrame.java (+11 -6)
-
src/dr/app/tracer/traces:
FrequencyPanel.java (+6),
JointDensityPanel.java (+1 -1)
-
src/dr/inference/trace:
AbstractTraceList.java (+2),
Trace.java (+5 -4),
TraceCorrelation.java (new),
TraceDistribution.java (+8 -5)
-
dong.w.xie
2011-02-25 11:56
#47
Rev.: 3830
-
87 lines of code changed in 12 files:
-
src/dr/app/tools:
SkylineReconstructor.java (+9 -9)
-
src/dr/app/tracer/analysis:
DemographicDialog.java (+46 -46),
GMRFSkyrideDialog.java (+4 -4)
-
src/dr/app/tracer/traces:
RawTracePanel.java (new)
-
src/dr/app/vcs:
VariableCoalescentSimulator.java (+5 -9)
-
src/dr/evolution/coalescent:
PLCoalescentSimulator.java (new)
-
src/dr/inference/trace:
DensityRectangle.java (new)
-
dong.w.xie
2011-02-25 10:44
#46
Rev.: 3829
-
12 lines of code changed in 2 files:
-
src/dr/app/tracer/analysis:
BayesianSkylineDialog.java (+10 -15)
-
src/dr/app/tracer/traces:
FilterDiscretePanel.java (+2)
-
rambaut
2011-02-25 05:13
#45
Rev.: 3828
-
6 lines of code changed in 1 file:
-
src/dr/evomodel/continuous:
MultidimensionalScalingLikelihood.java (+6 -3)
-
dong.w.xie
2011-02-24 16:56
#44
Rev.: 3827
-
39 lines of code changed in 4 files:
-
src/dr/app/tracer/traces:
FilterListPanel.java (+14 -3),
JointDensityPanel.java (+12 -4)
-
src/dr/inference/trace:
Trace.java (+12 -6),
TraceDistribution.java (+1 -1)
-
dong.w.xie
2011-02-24 13:06
#43
Rev.: 3826
-
39 lines of code changed in 1 file:
-
src/dr/app/tracer/application:
TracerFrame.java (+39 -15)
-
rambaut
2011-02-24 11:37
#42
Rev.: 3825
-
26 lines of code changed in 2 files:
-
src/dr/evomodel/continuous:
AntigenicTraitLikelihood.java (+1 -1),
MultidimensionalScalingLikelihood.java (+25 -20)
-
dong.w.xie
2011-02-24 11:07
#41
Rev.: 3824
-
77 lines of code changed in 6 files:
-
src/dr/app/tracer/application:
TracerFrame.java (+25 -7)
-
src/dr/app/tracer/traces:
CombinedTraces.java (+50 -11),
FilterDialog.java (new)
-
src/dr/inference/trace:
FilteredTraceList.java (+1 -1)
-
msuchard
2011-02-24 10:11
#40
Rev.: 3823
-
1 lines of code changed in 1 file:
-
src/dr/app/beagle/evomodel/treelikelihood:
BeagleTreeLikelihood.java (+1 -1)
-
rambaut
2011-02-24 05:15
#39
Rev.: 3822
-
254 lines of code changed in 3 files:
-
src/dr/app/phylogeography/tools:
TreeKMLGenerator.java (+14 -4)
-
src/dr/evomodel/continuous:
AntigenicTraitLikelihood.java (+50 -481),
MultidimensionalScalingLikelihood.java (+190 -164)
-
dong.w.xie
2011-02-23 16:30
#38
Rev.: 3821
-
104 lines of code changed in 5 files:
-
src/dr/app/tracer/application:
TracerFrame.java (+37 -116)
-
src/dr/app/tracer/traces:
FilterContinuousPanel.java (+26 -9),
FilterDialog.java (+19 -2),
FilterDiscretePanel.java (+1 -2),
FilterListPanel.java (+21 -33)
-
msuchard
2011-02-23 16:07
#37
Rev.: 3820
-
29 lines of code changed in 2 files:
-
src/dr/inferencexml/model:
MaskedParameterParser.java (+29 -2)
-
dong.w.xie
2011-02-23 11:49
#36
Rev.: 3818
-
47 lines of code changed in 6 files:
-
src/dr/app/tracer/application:
TracerFrame.java (-48)
-
src/dr/app/tracer/traces:
FilterAbstractPanel.java (+1 -1),
FilterDialog.java (+9 -7),
FilterDiscretePanel.java (+7 -1),
FilterListPanel.java (+28 -20)
-
src/dr/inference/trace:
Trace.java (+2 -2)
-
msuchard
2011-02-23 11:13
#35
Rev.: 3817
-
42 lines of code changed in 1 file:
-
src/dr/evomodel/continuous:
MultidimensionalScalingLikelihood.java (+42)
-
dong.w.xie
2011-02-22 20:54
#34
Rev.: 3816
-
64 lines of code changed in 4 files:
-
src/dr/app/tracer/application:
TracerFrame.java (+29 -25)
-
src/dr/app/tracer/traces:
FilterListPanel.java (+6 -12)
-
src/dr/inference/trace:
AbstractTraceList.java (+2 -1),
Trace.java (+27)
-
dong.w.xie
2011-02-22 13:52
#33
Rev.: 3815
-
138 lines of code changed in 6 files:
-
src/dr/app/tracer/application:
TracerFrame.java (+93 -69)
-
src/dr/app/tracer/traces:
CombinedTraces.java (+3 -1)
-
src/dr/inference/trace:
LogFileTraces.java (+41 -18),
Trace.java (+1 -1),
TraceList.java (new)
-
dong.w.xie
2011-02-21 15:14
#32
Rev.: 3814
-
91 lines of code changed in 5 files:
-
src/dr/app/tracer/application:
TracerFrame.java (+6 -1)
-
src/dr/app/tracer/traces:
FilterDialog.java (+8 -74),
FilterListPanel.java (+67 -30)
-
src/dr/inference/trace:
FilteredTraceList.java (+5),
TraceDistribution.java (+5 -1)
-
dong.w.xie
2011-02-21 12:20
#31
Rev.: 3813
-
270 lines of code changed in 7 files:
-
src/dr/app/tracer/application:
TracerFrame.java (+15 -7)
-
src/dr/app/tracer/traces:
FilterAbstractPanel.java (+27),
FilterContinuousPanel.java (+7 -4),
FilterDialog.java (+10 -187),
FilterDiscretePanel.java (+2 -1),
FilterListPanel.java (+209),
FilterPanel.java (del)
-
philippe.lemey@gmail.com
2011-02-20 05:06
#30
-
14 lines of code changed in 2 files:
-
src/dr/app/beagle/evomodel/parsers:
DnDsLoggerParser.java (+3 -1)
-
src/dr/app/beagle/evomodel/utilities:
DnDsLogger.java (+11 -3)
-
dong.w.xie
2011-02-18 16:08
#29
Rev.: 3810
-
483 lines of code changed in 11 files:
-
src/dr/app/tracer/application:
AnalysisMenuFactory.java (+13),
AnalysisMenuHandler.java (+2),
TracerFrame.java (+107 -98)
-
src/dr/app/tracer/traces:
FilterContinuousPanel.java (+37),
FilterDialog.java (+221 -184),
FilterDiscretePanel.java (+65),
FilterPanel.java (new 27)
-
src/dr/inference/trace:
Filter.java (+5 -14),
FilteredTraceList.java (+1),
Trace.java (+3 -8),
TraceFactory.java (+2 -2)
-
akaruiws
2011-02-18 15:10
#28
Rev.: 3809
-
0 lines of code changed in 1 file:
-
examples/moa:
logistics.xml (del)
-
dong.w.xie
2011-02-18 10:34
#27
Rev.: 3808
-
150 lines of code changed in 17 files:
-
src/dr/app/tools:
SkylineReconstructor.java (+9 -11)
-
src/dr/app/tracer/analysis:
BayesFactorsDialog.java (+1 -2),
BayesianSkylineDialog.java (+10 -9),
DemographicDialog.java (+53 -52),
GMRFSkyrideDialog.java (+5 -4),
TimeDensityDialog.java (new)
-
src/dr/app/tracer/traces:
CombinedTraces.java (-20)
-
src/dr/inference/trace:
ArrayTraceList.java (-18),
DensityRectangle.java (+5 -5),
LogFileTraces.java (-26),
MarginalLikelihoodAnalysis.java (+18 -15),
Trace.java (+5 -20),
TraceAnalysis.java (+5 -12),
TraceList.java (+32 -15)
-
src/dr/inferencexml/trace:
MarginalLikelihoodAnalysisParser.java (+2 -2)
-
dong.w.xie
2011-02-17 16:46
#26
Rev.: 3807
-
22 lines of code changed in 6 files:
-
src/dr/app/gui/chart:
FrequencyPlot.java (+1 -1)
-
src/dr/app/tracer/analysis:
DemographicDialog.java (-1)
-
src/dr/inference/trace:
OldDnDsPerSiteAnalysis.java (new),
PathSamplingAnalysis.java (+11 -15),
Trace.java (-35)
-
akaruiws
2011-02-17 15:37
#25
Rev.: 3806
-
1092 lines of code changed in 12 files:
-
examples/moa:
logistics.xml (new 377)
-
examples/release:
testMCMC.xml (new 1)
-
src/dr/app/beast:
development_parsers.properties (+1)
-
src/dr/evomodel/sitemodel:
GammaSiteBMA.java (new 262)
-
src/dr/evomodel/substmodel:
NtdBMA.java (+14 -8)
-
src/dr/evomodelxml/sitemodel:
GammaSiteBMAParser.java (new 77)
-
src/dr/evomodelxml/substmodel:
NtdBMAParser.java (new)
-
src/test/dr/evomodel/sitemodel:
testGammaSiteBMA.java (new 262)
-
src/test/dr/evomodel/substmodel:
testNtdBMA.java (new)
-
dong.w.xie
2011-02-17 15:31
#24
Rev.: 3805
-
404 lines of code changed in 38 files:
-
src/dr/app/gui/chart:
AreaPlot.java (+4 -3),
CategoryDensityPlot.java (+9 -8),
FrequencyPlot.java (+20 -19),
KDENumericalDensityPlot.java (+3 -1),
LinePlot.java (+2 -1),
NumericalDensityPlot.java (+5 -5),
Plot.java (+4 -3),
RegressionPlot.java (+3 -2),
ScatterPlot.java (+2 -1)
-
src/dr/app/pathogen:
ParentPlot.java (+8 -2),
TreesPanel.java (+13 -15)
-
src/dr/app/tools:
SkylineReconstructor.java (+2 -1),
TimeSlicer.java (+2 -1)
-
src/dr/app/tracer/analysis:
BayesianSkylineDialog.java (+2 -1),
DemographicDialog.java (+2 -4),
GMRFSkyrideDialog.java (+2 -1),
LineagesThroughTimeDialog.java (+2 -1),
TraitThroughTimeDialog.java (+2 -1)
-
src/dr/app/tracer/application:
TracerFrame.java (+9 -9)
-
src/dr/app/tracer/traces:
BetterDensityPanel.java (new 8),
CombinedTraces.java (+1 -1),
DensityPanel.java (+19 -28),
FilterDialog.java (+3 -3),
FrequencyPanel.java (+13 -15),
JTraceChart.java (+19 -21),
JointDensityPanel.java (+17 -15),
RawTracePanel.java (+27 -27),
SummaryStatisticsPanel.java (+12 -12)
-
src/dr/inference/loggers:
ArrayLogFormatter.java (+2 -1)
-
src/dr/inference/trace:
AbstractTraceList.java (+2 -1),
Filter.java (+1 -1),
LogFileTraces.java (+22 -25),
Trace.java (+25 -23),
TraceCorrelation.java (+5 -5),
TraceDistribution.java (+121 -136),
TraceFactory.java (+4 -4)
-
src/dr/stats:
Variate.java (+7)
-
dong.w.xie
2011-02-16 16:32
#23
Rev.: 3804
-
482 lines of code changed in 33 files:
-
src/dr/app/coalgen:
CoalGenApp.java (new),
CoalGenFrame.java (+1 -2)
-
src/dr/app/gui/chart:
KDENumericalDensityPlot.java (+3 -3)
-
src/dr/app/tools:
SkylineReconstructor.java (+1 -2),
TimeSlicer.java (+2 -2),
TreeAnnotator.java (+1 -1)
-
src/dr/app/tracer/analysis:
BayesianSkylineDialog.java (+2 -2),
DemographicDialog.java (+3 -4),
GMRFSkyrideDialog.java (+2 -2),
LineagesThroughTimeDialog.java (+2 -2),
TraitThroughTimeDialog.java (+2 -2)
-
src/dr/app/tracer/application:
TracerFrame.java (+13 -12)
-
src/dr/app/tracer/traces:
BetterDensityPanel.java (+5 -2),
CombinedTraces.java (+14 -28),
DensityPanel.java (+18 -11),
FrequencyPanel.java (+12 -9),
JointDensityPanel.java (+23 -23),
RawTracePanel.java (+31 -39)
-
src/dr/inference/loggers:
ArrayLogFormatter.java (+1 -2)
-
src/dr/inference/trace:
AbstractTraceList.java (+1 -1),
ArrayTraceList.java (+4 -4),
DnDsPerSiteAnalysis.java (+2 -2),
FilteredTraceList.java (+3 -3),
LogFileTraces.java (+129 -124),
Trace.java (+134 -79),
TraceCorrelation.java (+10 -14),
TraceDistribution.java (+13 -38),
TraceFactory.java (+18 -18),
TraceList.java (+10 -3)
-
src/dr/inferencexml/trace:
TraceAnalysisParser.java (new)
-
msuchard
2011-02-16 10:34
#22
Rev.: 3803
-
5 lines of code changed in 2 files:
-
src/dr/app/beagle/tools:
CompleteHistorySimulator.java (+1 -1)
-
src/dr/evolution/alignment:
SimpleAlignment.java (+4 -1)
-
akaruiws
2011-02-15 17:04
#21
Rev.: 3802
-
59 lines of code changed in 1 file:
-
src/test/dr/evomodel/substmodel:
testNtdBMA.java (+59 -12)
-
akaruiws
2011-02-15 16:17
#20
Rev.: 3801
-
11 lines of code changed in 1 file:
-
src/test/dr/evomodel/substmodel:
testNtdBMA.java (+11 -9)
-
akaruiws
2011-02-15 15:29
#19
Rev.: 3800
-
227 lines of code changed in 1 file:
-
src/test/dr/evomodel/substmodel:
testNtdBMA.java (+227)
-
akaruiws
2011-02-15 14:01
#18
Rev.: 3799
-
27 lines of code changed in 1 file:
-
src/dr/evomodel/substmodel:
NtdBMA.java (+27)
-
akaruiws
2011-02-15 13:00
#17
Rev.: 3798
-
157 lines of code changed in 3 files:
-
src/dr/app/beast:
development_parsers.properties (+1)
-
src/dr/evomodel/substmodel:
NtdBMA.java (+83)
-
src/dr/evomodelxml/substmodel:
NtdBMAParser.java (+73)
-
msuchard
2011-02-15 09:54
#16
Rev.: 3797
-
36 lines of code changed in 2 files:
-
src/dr/app/beagle/tools:
CompleteHistorySimulator.java (+29 -1)
-
src/dr/app/beagle/tools/parsers:
CompleteHistorySimulatorParser.java (+7)
-
dong.w.xie
2011-02-15 09:08
#15
Rev.: 3796
-
478 lines of code changed in 50 files:
-
src/dr/app/gui/chart:
AreaPlot.java (+13 -13),
CategoryDensityPlot.java (+9 -9),
DensityEstimatePlot.java (+4 -4),
FrequencyPlot.java (+19 -19),
KDENumericalDensityPlot.java (+12 -12),
LineDistributionPlot.java (+2 -2),
LinePlot.java (+5 -5),
NumericalDensityPlot.java (+6 -6),
Plot.java (+16 -14),
RegressionPlot.java (+2 -2),
ScatterPlot.java (+4 -4)
-
src/dr/app/pathogen:
ParentPlot.java (+12 -13),
TreesPanel.java (+55 -41)
-
src/dr/app/tools:
SkylineReconstructor.java (+10 -7)
-
src/dr/app/tracer/analysis:
BayesFactorsDialog.java (+2 -5),
BayesianSkylineDialog.java (+10 -10),
DemographicDialog.java (+9 -9),
DemographicPlotPanel.java (+4 -4),
GMRFSkyrideDialog.java (+10 -10),
LineagesThroughTimeDialog.java (+10 -10),
TemporalAnalysisPlotPanel.java (+4 -4),
TimeDensityDialog.java (+3 -3),
TraitThroughTimeDialog.java (+10 -10)
-
src/dr/app/tracer/traces:
BetterDensityPanel.java (+1 -2),
DensityPanel.java (+4 -4),
FrequencyPanel.java (+3 -3),
JTraceChart.java (+8 -8),
JointDensityPanel.java (+2 -2),
RawTracePanel.java (+20 -20)
-
src/dr/evolution/tree:
LineageCountThroughTime.java (new)
-
src/dr/inference/trace:
DensityEstimate.java (new),
KernelDensityEstimate.java (+4 -7),
MarginalLikelihoodAnalysis.java (+8 -8),
Trace.java (+38 -1),
TraceAnalysis.java (+6 -10)
-
src/dr/inferencexml/trace:
MarginalLikelihoodAnalysisParser.java (+2 -5),
TraceAnalysisParser.java (+7 -3)
-
src/dr/math/distributions:
BetaKDEDistribution.java (new),
GammaKDEDistribution.java (+2 -2),
KernelDensityEstimatorDistribution.java (+10 -3),
NormalKDEDistribution.java (+6 -6)
-
src/dr/stats:
Regression.java (+7 -7),
Variate.java (+96 -211)
-
src/test/dr/math:
KDEDistributionTest.java (+2 -3)
-
rambaut
2011-02-15 05:09
#14
Rev.: 3795
-
173 lines of code changed in 3 files:
-
src/dr/app/treespace:
CladeSystem.java (+73 -8),
TreeSpaceFrame.java (+98 -8)
-
src/dr/evomodel/continuous:
AntigenicTraitLikelihood.java (+2 -3)
-
rambaut
2011-02-14 19:56
#13
Rev.: 3794
-
10 lines of code changed in 1 file:
-
src/dr/evomodel/continuous:
AntigenicTraitLikelihood.java (+10 -1)
-
alexei.drummond
2011-02-12 17:51
#12
Rev.: 3793
-
334 lines of code changed in 1 file:
-
src/dr/evomodel/speciation:
BirthDeathSerialSkylineModel.java (+334)
-
rambaut
2011-02-09 05:18
#11
Rev.: 3792
-
46 lines of code changed in 5 files:
-
build_pathogen.xml (+1 -1)
-
src/dr/app/pathogen:
PathogenApp.java (new)
-
src/dr/app/phylogeography/tools:
TreeDensityKML.java (+44 -12)
-
rambaut
2011-02-09 05:17
#10
Rev.: 3791
-
166 lines of code changed in 5 files:
-
src/dr/evomodel/branchratemodel:
ArbitraryBranchRates.java (+1 -1)
-
src/dr/evomodel/continuous:
AbstractMultivariateTraitLikelihood.java (+13 -10),
AntigenicTraitLikelihood.java (+150 -94)
-
src/dr/evomodel/tree:
EmpiricalTreeDistributionModel.java (-1),
TreeParameterModel.java (+2 -3)
-
rambaut
2011-02-07 23:33
#9
Rev.: 3790
-
211 lines of code changed in 2 files:
-
src/dr/evomodel/continuous:
AntigenicTraitLikelihood.java (+105 -127)
-
src/dr/util:
DataTable.java (+106 -1)
-
dong.w.xie
2011-02-04 16:36
#8
Rev.: 3789
-
8 lines of code changed in 1 file:
-
src/dr/inference/trace:
Trace.java (+8 -5)
-
dong.w.xie
2011-02-04 12:48
#7
Rev.: 3788
-
1 lines of code changed in 2 files:
-
src/dr/evomodel/speciation:
ModelAveragingSpeciationLikelihood.java (new)
-
dong.w.xie
2011-02-04 10:09
#6
Rev.: 3787
-
55 lines of code changed in 10 files:
-
src/dr/app/tracer/application:
TracerFrame.java (+1 -1)
-
src/dr/app/tracer/traces:
BetterDensityPanel.java (+1 -1),
DensityPanel.java (+6 -6),
FrequencyPanel.java (+5 -5),
JointDensityPanel.java (+7 -25),
RawTracePanel.java (+11 -11)
-
src/dr/inference/trace:
OldDnDsPerSiteAnalysis.java (+2 -2),
Trace.java (+9 -113),
TraceDistribution.java (+11)
-
src/dr/inferencexml/trace:
TraceAnalysisParser.java (+2 -2)
-
rambaut
2011-02-04 04:23
#5
Rev.: 3786
-
3 lines of code changed in 4 files:
-
src/dr/evoxml:
ConstantPatternsParser.java (new),
MergePatternsParser.java (new)
-
dong.w.xie
2011-02-03 16:30
#4
Rev.: 3785
-
393 lines of code changed in 24 files:
-
src/dr/app/gui/chart:
FrequencyPlot.java (+2 -2)
-
src/dr/app/tracer/analysis:
BayesFactorsDialog.java (+8 -9)
-
src/dr/app/tracer/application:
TracerFrame.java (+35 -34)
-
src/dr/app/tracer/traces:
BetterDensityPanel.java (+6 -6),
CombinedTraces.java (+13 -27),
DensityPanel.java (+10 -22),
FilterDialog.java (+16 -18),
FrequencyPanel.java (+8 -18),
JointDensityPanel.java (+57 -172),
RawTracePanel.java (+17 -41),
SummaryStatisticsPanel.java (+8 -8)
-
src/dr/inference/trace:
AbstractTraceList.java (+13 -12),
ArrayTraceList.java (+9 -14),
DnDsPerSiteAnalysis.java (+1 -1),
Filter.java (+22 -45),
FilteredTraceList.java (+46 -51),
LogFileTraces.java (+17 -29),
PathSamplingAnalysis.java (+2 -2),
Trace.java (+57 -22),
TraceCorrelation.java (-14),
TraceDistribution.java (+39 -62),
TraceList.java (+3 -22)
-
src/dr/inferencexml/trace:
MarginalLikelihoodAnalysisParser.java (+1 -1),
TraceAnalysisParser.java (+3 -1)
-
rambaut
2011-02-02 08:07
#3
Rev.: 3784
-
94 lines of code changed in 2 files:
-
src/dr/app/beast:
release_parsers.properties (+1)
-
src/dr/evoxml:
ConstantPatternsParser.java (+93)
-
rambaut
2011-02-02 01:48
#2
Rev.: 3783
-
512 lines of code changed in 2 files:
-
src/dr/app/beast:
development_parsers.properties (+1)
-
src/dr/evomodel/continuous:
MultidimensionalScalingLikelihood.java (+511)
-
msuchard
2011-02-01 02:27
#1
Rev.: 3782
-
2 lines of code changed in 1 file:
-
src/dr/evomodel/continuous:
AbstractMultivariateTraitLikelihood.java (+2 -2)