-
msuchard
2010-06-30 10:13
#89
Rev.: 3297
-
48 lines of code changed in 5 files:
-
src/dr/app/tracer/application:
TracerApp.java (+9 -3)
-
src/dr/gui/chart:
KDENumericalDensityPlot.java (+12 -1)
-
src/dr/math/distributions:
KernelDensityEstimatorDistribution.java (+23),
NormalKDEDistribution.java (+4)
-
msuchard
2010-06-30 00:27
#88
Rev.: 3296
-
418 lines of code changed in 4 files:
-
src/dr/geo:
KernelDensityEstimator2D.java (+1 -1)
-
src/dr/math:
ComplexArray.java (new 59),
FastFourierTransform.java (new 151)
-
src/dr/math/distributions:
NormalKDEDistribution.java (+207 -4)
-
philippe.lemey@gmail.com
2010-06-29 11:28
#87
Rev.: 3295
-
136 lines of code changed in 5 files:
-
src/dr/geo:
GeoMultiSpatialCollectionModel.java (del),
GeoMultiSpatialDistribution.java (del),
GeoSpatialDistribution.java (+1),
Polygon.java (new 110),
Polygon2D.java (+25)
-
philippe.lemey@gmail.com
2010-06-29 10:31
#86
Rev.: 3294
-
0 lines of code changed in 1 file:
-
src/dr/geo:
GeoMultiSpatialDistribution.java (new)
-
philippe.lemey@gmail.com
2010-06-29 10:29
#85
Rev.: 3293
-
0 lines of code changed in 1 file:
-
src/dr/geo:
GeoMultiSpatialCollectionModel.java (new)
-
philippe.lemey@gmail.com
2010-06-28 17:01
#84
Rev.: 3292
-
321 lines of code changed in 1 file:
-
src/dr/inference/trace:
DnDsPerSiteAnalysis.java (+321 -165)
-
msuchard
2010-06-26 08:11
#83
Rev.: 3291
-
76 lines of code changed in 3 files:
-
src/dr/app/beauti/options:
PartitionClockModel.java (+16 -3)
-
src/dr/app/beauti/siteModelsPanel:
PartitionModelPanel.java (+4 -1)
-
src/dr/math/distributions:
NormalKDEDistribution.java (+56)
-
msuchard
2010-06-26 05:42
#82
Rev.: 3290
-
42 lines of code changed in 1 file:
-
src/dr/app/beagle/evomodel/substmodel:
CodonPartitionedRobustCounting.java (+42 -34)
-
msuchard
2010-06-25 15:58
#81
Rev.: 3289
-
102 lines of code changed in 4 files:
-
src/dr/app/beagle/evomodel/substmodel:
CodonPartitionedRobustCounting.java (+77 -6),
MarkovJumpsSubstitutionModel.java (+19 -6),
UniformizedSubstitutionModel.java (+2 -6)
-
src/dr/math/distributions:
KernelDensityEstimatorDistribution.java (+4)
-
akaruiws
2010-06-25 15:04
#80
Rev.: 3288
-
0 lines of code changed in 1 file:
-
examples/mountainLion:
mountainLion.xml (del)
-
dong.w.xie
2010-06-25 12:28
#79
Rev.: 3287
-
2 lines of code changed in 3 files:
-
examples/Phylogeography:
H5N1_HA_discrete.xml (+1 -1),
H5N1_HA_discrete_traits.xml (+1 -1)
-
dong.w.xie
2010-06-25 12:04
#78
Rev.: 3286
-
2 lines of code changed in 1 file:
-
src/dr/app/beauti/generator:
SubstitutionModelGenerator.java (+2 -2)
-
dong.w.xie
2010-06-25 10:23
#77
Rev.: 3285
-
5 lines of code changed in 1 file:
-
src/dr/evomodelxml/substmodel:
GeneralSubstitutionModelParser.java (+5)
-
rambaut
2010-06-25 03:24
#76
Rev.: 3284
-
870 lines of code changed in 7 files:
-
src/dr/app/tracer/traces:
BetterDensityPanel.java (+6 -10),
CorrelationPanel.java (del),
DensityPanel.java (+191 -113),
FrequencyPanel.java (+3 -3),
JointDensityPanel.java (+663),
RawTracePanel.java (+1 -1),
TracePanel.java (+6 -6)
-
dong.w.xie
2010-06-24 11:51
#75
Rev.: 3283
-
6 lines of code changed in 1 file:
-
src/dr/app/beauti/util:
BEAUTiImporter.java (+6 -2)
-
msuchard
2010-06-24 03:52
#74
Rev.: 3281
-
110 lines of code changed in 5 files:
-
src/dr/app/beagle/evomodel/parsers:
CodonPartitionedRobustCountingParser.java (+12 -4)
-
src/dr/app/beagle/evomodel/substmodel:
CodonPartitionedRobustCounting.java (+39 -16)
-
src/dr/evolution/tree:
TreeTrait.java (+34 -11)
-
src/dr/inference/markovjumps:
StateHistory.java (+12 -2),
SubordinatedProcess.java (+13 -1)
-
msuchard
2010-06-23 15:55
#73
Rev.: 3280
-
41 lines of code changed in 4 files:
-
src/dr/app/beagle/evomodel/parsers:
CodonPartitionedRobustCountingParser.java (+5)
-
src/dr/app/beagle/evomodel/substmodel:
CodonPartitionedRobustCounting.java (+31 -7),
MarkovJumpsSubstitutionModel.java (+4),
UniformizedSubstitutionModel.java (+1 -2)
-
msuchard
2010-06-23 02:16
#72
Rev.: 3279
-
3 lines of code changed in 1 file:
-
src/dr/app/tracer/traces:
TracePanel.java (+3 -1)
-
msuchard
2010-06-22 16:09
#71
Rev.: 3278
-
500 lines of code changed in 7 files:
-
src/dr/app/beagle/evomodel/parsers:
StratifiedTraitLoggerParser.java (+1 -3)
-
src/dr/app/tracer/traces:
BetterDensityPanel.java (+77),
DensityPanel.java (+35 -26),
TracePanel.java (+13)
-
src/dr/gui/chart:
KDENumericalDensityPlot.java (+177),
KDESetupDialog.java (new 190)
-
src/dr/math/distributions:
GammaKDEDistribution.java (+7 -4)
-
msuchard
2010-06-22 05:50
#70
Rev.: 3277
-
360 lines of code changed in 3 files:
-
src/dr/app/beagle/evomodel/substmodel:
ProductChainSubstitutionModel.java (+7 -7)
-
src/dr/evomodel/continuous:
AbstractMultivariateTraitLikelihood.java (+15 -300)
-
src/dr/evomodelxml/treelikelihood:
TreeTraitParserUtilities.java (+338)
-
dong.w.xie
2010-06-21 18:03
#69
Rev.: 3276
-
3 lines of code changed in 2 files:
-
src/dr/app/beauti/generator:
LogGenerator.java (+1 -1)
-
src/dr/app/beauti/options:
BeautiOptions.java (+2 -1)
-
akaruiws
2010-06-18 18:45
#68
Rev.: 3275
-
1311 lines of code changed in 14 files:
-
examples/Phylogeography/continuous:
RacRABV_homogeneous.xml (+4 -2)
-
examples/mountainLion:
mountainLion.xml (new 1072)
-
src/dr/app/beast:
development_parsers.properties (+4 -1)
-
src/dr/evomodel/substmodel:
MicrosatelliteModel.java (+48 -2)
-
src/dr/evomodel/tree:
MicrosatelliteSamplerTreeModel.java (+2 -2)
-
src/dr/evomodel/treelikelihood:
MicrosatelliteSamplerTreeLikelihood.java (new)
-
src/dr/inference/operators:
MsatFullAncestryImportanceSamplingOperator.java (new 101)
-
src/dr/inferencexml/operators:
MicrosatelliteAveragingOperatorParser.java (new 2),
MsatFullAncestryImportanceSamplingOperatorParser.java (new 49)
-
src/test/dr/evomodel/substmodel:
AsymQuadTest.java (+8 -1),
LinearBiasTest.java (+7),
TwoPhaseModelTest.java (+6 -1)
-
dong.w.xie
2010-06-17 12:39
#67
Rev.: 3274
-
45 lines of code changed in 2 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+7 -4),
LogGenerator.java (+38 -29)
-
msuchard
2010-06-17 10:45
#66
Rev.: 3273
-
408 lines of code changed in 16 files:
-
examples:
testRobustCounting.xml (new 2)
-
src/dr/app/beagle/evomodel/parsers:
StratifiedTraitLoggerParser.java (+50 -13)
-
src/dr/app/beagle/evomodel/substmodel:
CodonPartitionedRobustCounting.java (+91 -106),
StratifiedTraitOutputFormat.java (+13 -6)
-
src/dr/app/beagle/evomodel/treelikelihood:
MarkovJumpsBeagleTreeLikelihood.java (+1 -2)
-
src/dr/app/beagle/evomodel/utilities:
StratifiedTraitLogger.java (del),
TreeTraitLogger.java (+68)
-
src/dr/evolution/tree:
Tree.java (+1 -1),
TreeTrait.java (+149 -19),
TreeTraitProvider.java (+3)
-
src/dr/evomodel/branchratemodel:
AbstractBranchRateModel.java (+4),
DefaultBranchRateModel.java (+4)
-
src/dr/evomodel/continuous:
BivariateTraitBranchAttributeProvider.java (new)
-
src/dr/evomodel/tree:
TreeParameterModel.java (+4)
-
src/dr/evomodelxml/tree:
TreeLoggerParser.java (+17 -2)
-
msuchard
2010-06-17 03:21
#65
Rev.: 3272
-
113 lines of code changed in 3 files:
-
src/dr/app/beagle/evomodel/parsers:
EmpiricalAminoAcidModelParser.java (+71)
-
src/dr/app/beagle/evomodel/substmodel:
EmpiricalAminoAcidModel.java (+41)
-
src/dr/app/beast:
beagle_parsers.properties (+1)
-
msuchard
2010-06-16 13:54
#64
Rev.: 3271
-
172 lines of code changed in 1 file:
-
src/dr/evolution/tree:
TreeTrait.java (+172 -7)
-
dong.w.xie
2010-06-15 11:59
#63
Rev.: 3270
-
6 lines of code changed in 1 file:
-
src/dr/app/beauti:
BeautiFrame.java (+6 -4)
-
msuchard
2010-06-15 09:39
#62
Rev.: 3269
-
6 lines of code changed in 3 files:
-
src/dr/app/beagle/evomodel/substmodel:
MarkovJumpsSubstitutionModel.java (+3),
UniformizedSubstitutionModel.java (+2 -1)
-
src/dr/inference/markovjumps:
StateHistory.java (+1 -1)
-
msuchard
2010-06-15 08:26
#61
Rev.: 3268
-
50 lines of code changed in 6 files:
-
src/dr/app/beagle/evomodel/substmodel:
MarkovJumpsSubstitutionModel.java (+1 -1),
UniformizedSubstitutionModel.java (+10)
-
src/dr/app/beagle/evomodel/treelikelihood:
MarkovJumpsBeagleTreeLikelihood.java (+5 -2)
-
src/dr/evomodel/branchratemodel:
DiscreteTraitBranchRateModel.java (-3)
-
src/dr/inference/markovjumps:
StateHistory.java (+1 -1),
SubordinatedProcess.java (+33 -1)
-
msuchard
2010-06-15 06:49
#60
Rev.: 3267
-
23 lines of code changed in 4 files:
-
src/dr/app/beagle/evomodel/parsers:
MarkovJumpsTreeLikelihoodParser.java (+8 -7)
-
src/dr/app/beagle/evomodel/treelikelihood:
AncestralStateBeagleTreeLikelihood.java (+1),
MarkovJumpsBeagleTreeLikelihood.java (+13 -9)
-
src/dr/evomodel/branchratemodel:
DiscreteTraitBranchRateModel.java (+1 -1)
-
msuchard
2010-06-14 15:14
#59
Rev.: 3266
-
21 lines of code changed in 2 files:
-
src/dr/app/beagle/evomodel/treelikelihood:
AbstractTreeLikelihood.java (+1 -1),
AncestralStateBeagleTreeLikelihood.java (+20 -9)
-
msuchard
2010-06-14 14:48
#58
Rev.: 3265
-
1 lines of code changed in 1 file:
-
src/dr/evomodelxml/branchratemodel:
DiscreteTraitBranchRateModelParser.java (+1 -1)
-
msuchard
2010-06-14 14:20
#57
Rev.: 3264
-
85 lines of code changed in 7 files:
-
src/dr/app/beagle/evomodel/parsers:
AncestralStateTreeLikelihoodParser.java (+2 -1)
-
src/dr/app/beagle/evomodel/treelikelihood:
AncestralStateBeagleTreeLikelihood.java (+7 -8),
MarkovJumpsBeagleTreeLikelihood.java (+38 -8)
-
src/dr/app/beast:
development_parsers.properties (+1 -1)
-
src/dr/evomodel/branchratemodel:
DiscreteTraitBranchRateModel.java (+34 -29)
-
src/dr/evomodel/treelikelihood:
AncestralStateTreeLikelihood.java (+2 -2)
-
src/dr/evomodelxml/treelikelihood:
AncestralStateTreeLikelihoodParser.java (+1 -1)
-
dong.w.xie
2010-06-14 12:47
#56
Rev.: 3263
-
16 lines of code changed in 2 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+6 -3)
-
src/dr/evomodelxml/substmodel:
GeneralSubstitutionModelParser.java (+10 -3)
-
rambaut
2010-06-13 23:31
#55
Rev.: 3262
-
79 lines of code changed in 3 files:
-
src/dr/evomodel/branchratemodel:
LocalClockModel.java (+56 -21)
-
src/dr/evomodelxml/branchratemodel:
LocalClockModelParser.java (+23 -1)
-
akaruiws
2010-06-13 21:50
#54
Rev.: 3261
-
309 lines of code changed in 6 files:
-
src/dr/app/beast:
release_parsers.properties (+2)
-
src/dr/inference/operators:
RandomWalkIntegerNodeHeightWeightedOperator.java (+81),
RandomWalkIntegerOperator.java (+1 -1),
RandomWalkIntegerSetSizeWeightedOperator.java (+104)
-
src/dr/inferencexml/operators:
RandomWalkIntegerNodeHeightWeightedOperatorParser.java (new 59),
RandomWalkIntegerSetSizeWeightedOperatorParser.java (new 62)
-
dong.w.xie
2010-06-13 20:06
#53
Rev.: 3260
-
26 lines of code changed in 3 files:
-
src/dr/app/tracer/application:
TracerFrame.java (+2 -2)
-
src/dr/inference/trace:
LogFileTraces.java (+17 -19),
Trace.java (+7)
-
msuchard
2010-06-13 05:51
#52
Rev.: 3259
-
8 lines of code changed in 1 file:
-
src/dr/app/beagle/evomodel/substmodel:
UniformizedSubstitutionModel.java (+8 -2)
-
msuchard
2010-06-13 04:48
#51
Rev.: 3258
-
80 lines of code changed in 3 files:
-
src/dr/app/beagle/evomodel/substmodel:
MarkovJumpsSubstitutionModel.java (+33 -6)
-
src/dr/inference/markovjumps:
MarkovJumpsCore.java (new)
-
rambaut
2010-06-13 03:10
#50
Rev.: 3257
-
1 lines of code changed in 1 file:
-
src/dr/evomodel/branchratemodel:
DiscreteTraitBranchRateModel.java (+1 -1)
-
rambaut
2010-06-13 03:05
#49
Rev.: 3256
-
12 lines of code changed in 2 files:
-
src/dr/evomodel/branchratemodel:
DiscreteTraitBranchRateModel.java (+11 -11)
-
src/dr/evomodelxml/branchratemodel:
DiscreteTraitBranchRateModelParser.java (+1 -1)
-
rambaut
2010-06-12 22:52
#48
Rev.: 3255
-
54 lines of code changed in 2 files:
-
src/dr/evomodel/branchratemodel:
DiscreteTraitBranchRateModel.java (+44 -22)
-
src/dr/evomodelxml/branchratemodel:
DiscreteTraitBranchRateModelParser.java (+10 -3)
-
rambaut
2010-06-12 22:09
#47
Rev.: 3254
-
43 lines of code changed in 4 files:
-
src/dr/evolution/parsimony:
FitchParsimony.java (+4)
-
src/dr/evomodel/branchratemodel:
DiscreteTraitBranchRateModel.java (+31 -8)
-
src/dr/evomodelxml/branchratemodel:
DiscreteTraitBranchRateModelParser.java (+8 -1)
-
rambaut
2010-06-12 03:59
#46
Rev.: 3253
-
4 lines of code changed in 1 file:
-
src/dr/inference/model:
CompoundLikelihood.java (+4)
-
rambaut
2010-06-12 03:51
#45
Rev.: 3252
-
20 lines of code changed in 3 files:
-
src/dr/inference/mcmc:
MCMC.java (+1 -1)
-
src/dr/inference/model:
CompoundLikelihood.java (+18 -4)
-
src/dr/inferencexml:
MCMCParser.java (+1 -1)
-
dong.w.xie
2010-06-11 18:47
#44
Rev.: 3251
-
1 lines of code changed in 2 files:
-
doc:
New Tracer.docx (changed)
-
src/dr/app/tracer/traces:
FrequencyPanel.java (+1 -1)
-
akaruiws
2010-06-11 17:33
#43
Rev.: 3250
-
5 lines of code changed in 2 files:
-
src/dr/app/beast:
release_parsers.properties (+1 -1)
-
src/dr/inference/operators:
MicrosatelliteAveragingOperator.java (new 4)
-
dong.w.xie
2010-06-11 16:50
#42
Rev.: 3249
-
110 lines of code changed in 3 files:
-
src/dr/app/tracer/application:
TracerFrame.java (+91 -66)
-
src/dr/app/tracer/traces:
FilterDialog.java (+1 -1)
-
src/dr/inference/trace:
LogFileTraces.java (+18 -16)
-
akaruiws
2010-06-11 12:47
#41
Rev.: 3248
-
962 lines of code changed in 13 files:
-
src/dr/app/beast:
release_parsers.properties (+5)
-
src/dr/app/seqgen:
MicrosatelliteSimulator.java (+2 -4)
-
src/dr/evomodel/substmodel:
MsatAveragingSubsetModel.java (new 214)
-
src/dr/evomodelxml/substmodel:
MsatAveragingSubsetModelParser.java (new 252)
-
src/dr/inference/distribution:
DistributionLikelihood.java (+1 -1),
ModelSpecificPseudoPriorLikelihood.java (new 53),
TwoPartsDistributionLikelihood.java (new 54)
-
src/dr/inference/operators:
MicrosatelliteAveragingOperator.java (+111),
MicrosatelliteModelSelectOperator.java (+42)
-
src/dr/inferencexml/distribution:
ModelSpecificPseudoPriorLikelihoodParser.java (new 70),
TwoPartsDistributionLikelihoodParser.java (new 68)
-
src/dr/inferencexml/operators:
MicrosatelliteAveragingOperatorParser.java (+42),
MicrosatelliteModelSelectOperatorParser.java (new 48)
-
dong.w.xie
2010-06-11 00:01
#40
Rev.: 3247
-
84 lines of code changed in 4 files:
-
src/dr/app/tracer/application:
TracerFrame.java (+60 -21)
-
src/dr/app/tracer/traces:
FilterDialog.java (+16 -6)
-
src/dr/inference/trace:
Filter.java (+1 -1),
FilteredTraceList.java (+7 -2)
-
dong.w.xie
2010-06-10 11:43
#39
Rev.: 3246
-
19 lines of code changed in 2 files:
-
src/dr/app/tracer/traces:
FilterDialog.java (+17 -1)
-
src/dr/inference/trace:
Filter.java (+2 -1)
-
dong.w.xie
2010-06-09 15:51
#38
Rev.: 3245
-
42 lines of code changed in 1 file:
-
src/dr/app/tracer/traces:
FilterDialog.java (+42 -13)
-
dong.w.xie
2010-06-09 15:12
#37
Rev.: 3244
-
177 lines of code changed in 7 files:
-
src/dr/app/tracer/application:
TracerFrame.java (+3 -2)
-
src/dr/app/tracer/traces:
CorrelationPanel.java (new 117),
DensityPanel.java (+4 -17),
FrequencyPanel.java (+8 -13),
RawTracePanel.java (+23 -6)
-
src/dr/inference/trace:
LogFileTraces.java (+3 -3),
Trace.java (+19 -6)
-
dong.w.xie
2010-06-09 13:04
#36
Rev.: 3243
-
138 lines of code changed in 9 files:
-
src/dr/app/tracer/application:
TracerFrame.java (+1 -1)
-
src/dr/app/tracer/traces:
CombinedTraces.java (+30 -8),
DensityPanel.java (+10 -7),
FrequencyPanel.java (+11 -8)
-
src/dr/inference/trace:
ArrayTraceList.java (+12),
FilteredTraceList.java (+3),
LogFileTraces.java (+36 -8),
Trace.java (+10),
TraceList.java (+25)
-
dong.w.xie
2010-06-08 16:11
#35
Rev.: 3240
-
64 lines of code changed in 8 files:
-
src/dr/app/tracer/traces:
CombinedTraces.java (+5),
DensityPanel.java (+3 -3),
FilterDialog.java (+1),
FrequencyPanel.java (+3 -3)
-
src/dr/inference/trace:
ArrayTraceList.java (+4),
FilteredTraceList.java (+18 -1),
LogFileTraces.java (+11),
Trace.java (+19 -10)
-
dong.w.xie
2010-06-08 12:26
#34
Rev.: 3239
-
23 lines of code changed in 3 files:
-
src/dr/app/tracer/application:
TracerFrame.java (+2 -1)
-
src/dr/app/tracer/traces:
FilterDialog.java (+7 -4)
-
src/dr/inference/trace:
Filter.java (+14)
-
dong.w.xie
2010-06-08 11:36
#33
Rev.: 3238
-
68 lines of code changed in 3 files:
-
src/dr/app/tracer/traces:
DensityPanel.java (+27 -6),
FrequencyPanel.java (+11 -5)
-
src/dr/inference/trace:
Trace.java (+30 -8)
-
rambaut
2010-06-08 04:20
#32
Rev.: 3237
-
12 lines of code changed in 4 files:
-
src/dr/app/beagle/evomodel/treelikelihood:
AncestralStateBeagleTreeLikelihood.java (+1 -1),
MarkovJumpsBeagleTreeLikelihood.java (+3 -3)
-
src/dr/evomodel/branchratemodel:
DiscreteTraitBranchRateModel.java (+3 -3)
-
src/dr/inference/distribution:
MultivariateDistributionLikelihood.java (+5)
-
rambaut
2010-06-07 23:59
#31
Rev.: 3236
-
361 lines of code changed in 8 files:
-
src/dr/app/beast:
release_parsers.properties (+1 -1)
-
src/dr/evomodel/branchratemodel:
DiscreteTraitBranchRateModel.java (+269),
DiscreteTraitRateModel.java (del)
-
src/dr/evomodelxml/branchratemodel:
ContinuousTraitBranchRateModelParser.java (+1 -1),
DiscreteTraitBranchRateModelParser.java (+85)
-
src/dr/inference/mcmc:
MCMCOptions.java (+1 -1)
-
src/dr/inferencexml:
MCMCParser.java (+4 -2)
-
rambaut
2010-06-07 23:07
#30
Rev.: 3235
-
502 lines of code changed in 30 files:
-
src/dr/app/beagle/evomodel/substmodel:
CodonPartitionedRobustCounting.java (+30 -19)
-
src/dr/app/beagle/evomodel/treelikelihood:
AncestralStateBeagleTreeLikelihood.java (+11 -15),
MarkovJumpsBeagleTreeLikelihood.java (+4 -16)
-
src/dr/app/beagle/tools:
CompleteHistorySimulator.java (+2 -6)
-
src/dr/app/coalgen:
CoalGenApp.java (+171 -3),
CoalGenData.java (new),
CoalGenFrame.java (+2 -2)
-
src/dr/app/tools:
AncestralSequenceAnnotator.java (+2 -2),
ConvertMigrateTrees.java (+2 -4)
-
src/dr/evolution/tree:
Tree.java (+15 -14),
TreeTrait.java (+75 -61)
-
src/dr/evomodel/branchratemodel:
AbstractBranchRateModel.java (+4 -8),
DefaultBranchRateModel.java (+4 -4),
DiscreteTraitRateModel.java (new 41)
-
src/dr/evomodel/continuous:
AbstractMultivariateTraitLikelihood.java (+5 -23),
BivariateTraitBranchAttributeProvider.java (+5 -5)
-
src/dr/evomodel/ibd:
AvgPosteriorIBDReporter.java (+3 -7),
IBDReporter.java (new)
-
src/dr/evomodel/speciation:
RandomLocalYuleModel.java (+4 -12),
SpeciesTreeModel.java (+2 -6)
-
src/dr/evomodel/tree:
AncestralTrait.java (+1 -1),
TreeParameterModel.java (+26 -21),
WanderingTaxonLogger.java (+4 -8)
-
src/dr/evomodel/treelikelihood:
AncestralStateTreeLikelihood.java (+5 -13),
NodePosteriorTreeLikelihood.java (+5 -8)
-
rambaut
2010-06-07 23:04
#29
Rev.: 3234
-
17 lines of code changed in 1 file:
-
src/dr/inference/trace:
LogFileTraces.java (+17 -1)
-
akaruiws
2010-06-06 22:12
#28
Rev.: 3233
-
308 lines of code changed in 8 files:
-
examples:
Msat (new)
-
src/dr/app/seqgen:
MicrosatelliteSimulator.java (+3 -1)
-
src/dr/evomodel/tree:
TreeModel.java (+7 -3)
-
src/dr/evomodel/treelikelihood:
MicrosatelliteSamplerTreeLikelihood.java (+60 -18)
-
src/dr/evomodelxml/treelikelihood:
MicrosatelliteSamplerTreeLikelihoodParser.java (+25 -6)
-
src/dr/math:
MersenneTwisterFast.java (new)
-
src/test/dr/evomodel/substmodel:
MsatSamplingTreeLikelihoodTest.java (+212)
-
jheled
2010-06-06 20:49
#27
Rev.: 3232
-
33 lines of code changed in 4 files:
-
src/dr/evomodel/coalescent:
EBSPAnalysis.java (new)
-
src/dr/evomodelxml/coalescent:
EBSPAnalysisParser.java (+12 -1)
-
jheled
2010-06-06 20:48
#26
Rev.: 3231
-
3 lines of code changed in 1 file:
-
src/dr/inference/trace:
TraceFactory.java (+3 -3)
-
akaruiws
2010-06-06 16:23
#25
Rev.: 3230
-
201 lines of code changed in 8 files:
-
src/dr/evomodel/substmodel:
AsymmetricQuadraticModel.java (+40 -36),
LinearBiasModel.java (new),
MicrosatelliteModel.java (+78 -8),
OnePhaseModel.java (+7 -17),
TwoPhaseModel.java (+38 -22)
-
msuchard
2010-06-06 04:51
#24
Rev.: 3229
-
255 lines of code changed in 7 files:
-
src/dr/evolution/tree:
TreeTrait.java (+2 -2)
-
src/dr/evomodel/treelikelihood:
TreeLikelihood.java (+14)
-
src/test/dr/evomodel/treelikelihood:
AscertainmentCorrectedLikelihoodTest.java (+189),
LikelihoodTest.java (new)
-
src/test/dr/inference/trace:
TraceCorrelationAssert.java (+49)
-
msuchard
2010-06-05 10:41
#23
Rev.: 3226
-
37 lines of code changed in 1 file:
-
src/dr/evomodel/continuous:
AbstractMultivariateTraitLikelihood.java (+37 -14)
-
rambaut
2010-06-05 03:38
#22
Rev.: 3225
-
40 lines of code changed in 4 files:
-
src/dr/app/beagle/evomodel/treelikelihood:
MarkovJumpsBeagleTreeLikelihood.java (+31 -15)
-
src/dr/app/beast:
development_parsers.properties (-2),
release_parsers.properties (+3)
-
src/dr/evomodel/branchratemodel:
DiscreteTraitRateModel.java (+6 -6)
-
rambaut
2010-06-05 02:18
#21
Rev.: 3224
-
42 lines of code changed in 7 files:
-
build.xml (+4 -5),
build_tracer.xml (+1 -1)
-
lib:
beagle.jar (changed)
-
src/dr/app/beagle/evomodel/substmodel:
CodonPartitionedRobustCounting.java (+4)
-
src/dr/app/tracer/application:
TracerApp.java (+3 -3)
-
src/dr/evolution/tree:
Tree.java (+24 -22),
TreeTrait.java (+6)
-
dong.w.xie
2010-06-04 18:19
#20
Rev.: 3223
-
56 lines of code changed in 2 files:
-
src/dr/app/tracer/traces:
FrequencyPanel.java (+10 -5)
-
src/dr/inference/trace:
Trace.java (+46)
-
dong.w.xie
2010-06-04 15:56
#19
Rev.: 3222
-
25 lines of code changed in 2 files:
-
src/dr/app/beauti/treespanel:
PartitionTreeModelPanel.java (+11 -2)
-
src/dr/evolution/tree:
Tree.java (+14)
-
dong.w.xie
2010-06-03 11:33
#18
Rev.: 3221
-
54 lines of code changed in 4 files:
-
src/dr/app/beauti/treespanel:
PartitionTreeModelPanel.java (+44 -7),
TreesPanel.java (+1 -1)
-
src/dr/gui/tree:
JTreePanel.java (+9 -5)
-
msuchard
2010-06-03 06:20
#17
Rev.: 3220
-
17 lines of code changed in 1 file:
-
src/dr/app/beagle/evomodel/treelikelihood:
BeagleTreeLikelihood.java (+17 -17)
-
rambaut
2010-06-03 01:12
#16
Rev.: 3219
-
0 lines of code changed in 1 file:
-
src/dr/app/beagle/evomodel/branchratemodel:
MarkovJumpsBranchRateModel.java (del)
-
rambaut
2010-06-03 01:10
#15
Rev.: 3218
-
129 lines of code changed in 2 files:
-
src/dr/evomodel/branchratemodel:
DiscreteTraitRateModel.java (+126 -41)
-
src/dr/evomodelxml/tree:
AncestralTraitParser.java (+3 -3)
-
rambaut
2010-06-02 23:13
#14
Rev.: 3217
-
2 lines of code changed in 1 file:
-
src/dr/evolution/tree:
TreeTraitProvider.java (+2 -1)
-
rambaut
2010-06-02 23:10
#13
Rev.: 3216
-
169 lines of code changed in 5 files:
-
src/dr/app/beast:
release_parsers.properties (+2 -2)
-
src/dr/evomodel/tree:
AncestralTrait.java (+90)
-
src/dr/evomodel/treelikelihood:
AncestralState.java (del)
-
src/dr/evomodelxml/tree:
AncestralTraitParser.java (+77)
-
src/dr/evomodelxml/treelikelihood:
AncestralStateParser.java (del)
-
rambaut
2010-06-02 22:53
#12
Rev.: 3215
-
1160 lines of code changed in 44 files:
-
src/dr/app:
ConvertMigrateTrees.java (del)
-
src/dr/app/beagle/evomodel/substmodel:
CodonPartitionedRobustCounting.java (+35 -25)
-
src/dr/app/beagle/evomodel/treelikelihood:
AncestralStateBeagleTreeLikelihood.java (+41 -10),
MarkovJumpsBeagleTreeLikelihood.java (+25 -20)
-
src/dr/app/beagle/tools:
CompleteHistorySimulator.java (+36 -25)
-
src/dr/app/beast:
development_parsers.properties (-1),
release_parsers.properties (+3 -3)
-
src/dr/app/tools:
AncestralSequenceAnnotator.java (+3 -5),
ConvertMigrateTrees.java (+148)
-
src/dr/evolution/tree:
BranchAttributeProvider.java (del),
BranchRateProvider.java (del),
BranchRates.java (new 38),
NodeAttributeProvider.java (del),
Tree.java (+58 -68),
TreeTrait.java (+80),
TreeTraitProvider.java (+111)
-
src/dr/evomodel/arg:
OldTreeLogger.java (+2 -2)
-
src/dr/evomodel/branchratemodel:
BranchRateModel.java (+2 -2),
RandomLocalClockModel.java (-1)
-
src/dr/evomodel/continuous:
AbstractMultivariateTraitLikelihood.java (+64 -32),
BivariateTraitBranchAttributeProvider.java (+29 -8),
BranchDirectionAttributeProvider.java (new),
BranchMagnitudeAttributeProvider.java (+1 -2),
InhibitionAssayLikelihood.java (+1 -2)
-
src/dr/evomodel/ibd:
AvgPosteriorIBDReporter.java (+33 -13),
IBDReporter.java (+39 -7)
-
src/dr/evomodel/speciation:
RandomLocalYuleModel.java (+47 -13),
SpeciesTreeModel.java (+29 -10)
-
src/dr/evomodel/tree:
NodeTraitLogger.java (+5 -9),
TreeLogger.java (+13 -19),
TreeParameterModel.java (+26 -3),
WanderingTaxonLogger.java (+35 -15)
-
src/dr/evomodel/treelikelihood:
AncestralState.java (new 126),
AncestralStateTreeLikelihood.java (+42 -29),
NodePosteriorTreeLikelihood.java (+31 -11)
-
src/dr/evomodelxml:
WanderingTaxonLoggerParser.java (+1 -2)
-
src/dr/evomodelxml/tree:
TreeLoggerParser.java (+42 -45)
-
src/dr/evomodelxml/treelikelihood:
AncestralStateParser.java (new 10)
-
src/test/dr/evomodel/treelikelihood:
AncestralStateTreeLikelihoodTest.java (+3 -2)
-
dong.w.xie
2010-06-02 15:22
#11
Rev.: 3214
-
30 lines of code changed in 4 files:
-
src/dr/app/tracer/traces:
SummaryStatisticsPanel.java (+2 -2)
-
src/dr/gui/chart:
FrequencyPlot.java (new)
-
src/dr/inference/trace:
TraceDistribution.java (+27 -5)
-
dong.w.xie
2010-06-02 10:44
#10
Rev.: 3213
-
159 lines of code changed in 5 files:
-
src/dr/app/beauti/enumTypes:
StartingTreeType.java (+2 -2)
-
src/dr/app/beauti/generator:
InitialTreeGenerator.java (+44 -9)
-
src/dr/app/beauti/options:
PartitionTreeModel.java (+10)
-
src/dr/app/beauti/treespanel:
PartitionTreeModelPanel.java (+103 -87)
-
jheled
2010-06-02 07:05
#9
Rev.: 3212
-
16 lines of code changed in 1 file:
-
src/dr/inference/operators:
UniformIntegerOperator.java (+16 -6)
-
jheled
2010-06-02 07:04
#8
Rev.: 3211
-
7 lines of code changed in 10 files:
-
src/dr/evomodelxml/branchratemodel:
DiscretizedBranchRatesParser.java (+1 -1)
-
src/dr/evomodelxml/tree:
MonophylyStatisticParser.java (new),
NodeHeightsStatisticParser.java (+1 -1),
SpeciesTreeStatisticParser.java (new),
TreeLengthStatisticParser.java (new)
-
src/dr/inferencexml/model:
DummyLikelihoodParser.java (+2 -3)
-
jheled
2010-06-02 07:04
#7
Rev.: 3210
-
8 lines of code changed in 1 file:
-
src/dr/inferencexml/operators:
UniformIntegerOperatorParser.java (+8 -3)
-
jheled
2010-06-02 07:02
#6
Rev.: 3209
-
48 lines of code changed in 1 file:
-
src/dr/evomodelxml/tree:
TreeHeightStatisticParser.java (new 48)
-
jheled
2010-06-02 06:57
#5
Rev.: 3208
-
1 lines of code changed in 2 files:
-
src/dr/inferencexml/operators:
BitSwapOperatorParser.java (+1 -1)
-
rambaut
2010-06-02 00:12
#4
Rev.: 3207
-
882 lines of code changed in 60 files:
-
src/dr/app/beagle/evomodel/branchratemodel:
MarkovJumpsBranchRateModel.java (new)
-
src/dr/app/beast:
BeastParser.java (+1 -1),
release_parsers.properties (+3 -2)
-
src/dr/app/beauti/generator:
LogGenerator.java (+1 -1)
-
src/dr/app/oldbeauti:
BeastGenerator.java (+1 -1)
-
src/dr/app/tools:
AncestralSequenceAnnotator.java (+1 -1)
-
src/dr/evolution/tree:
BranchAttributeProvider.java (new 21),
BranchRateController.java (del),
BranchRateProvider.java (new 38),
NodeAttributeProvider.java (new 19),
Tree.java (+9 -9),
TreeTrait.java (+58),
TreeTraitProvider.java (+11)
-
src/dr/evomodel/arg:
ARGRelaxedClock.java (+2 -9),
OldTreeLogger.java (-125)
-
src/dr/evomodel/arg/branchratemodel:
ARGDiscretizedBranchRates.java (+2 -8)
-
src/dr/evomodel/branchratemodel:
AbstractBranchRateModel.java (+68),
ArbitraryBranchRates.java (+2 -10),
BranchRateModel.java (+4 -5),
ColouredTreeRateModel.java (del),
CompoundBranchRateModel.java (new),
ContinuousEpochBranchRateModel.java (new),
ContinuousTraitBranchRateModel.java (new 143),
DecayingRateModel.java (new),
DefaultBranchRateModel.java (+24 -9),
DiscreteTraitRateModel.java (+3 -15),
DiscretizedBranchRates.java (+1 -9),
LocalClockModel.java (+2 -10),
MixtureModelBranchRates.java (+1 -9),
RandomDiscretizedBranchRates.java (new 2),
RandomLocalClockModel.java (+19 -25),
RateEpochBranchRateModel.java (+3 -11),
ScaledTreeLengthRateModel.java (new),
StrictClockBranchRates.java (+2 -9),
TipBranchRateModel.java (+2 -11),
TraitBranchRateModel.java (del)
-
src/dr/evomodel/clock:
RateEvolutionLikelihood.java (+2 -9),
UniversalClock.java (new)
-
src/dr/evomodel/tree:
TreeLogger.java (+2 -2)
-
src/dr/evomodel/treelikelihood:
AncestralState.java (+1 -4),
AncestralStateTreeLikelihood.java (+23 -6)
-
src/dr/evomodelxml/branchratemodel:
ContinuousTraitBranchRateModelParser.java (+75),
TraitBranchRateModelParser.java (del)
-
src/dr/evomodelxml/coalescent:
DemographicLoggerParser.java (new 61)
-
src/dr/evomodelxml/tree:
TreeLoggerParser.java (+215)
-
src/dr/inferencexml/loggers:
DemographicLoggerParser.java (del),
TreeLoggerParser.java (del)
-
src/test/dr/evomodel/treelikelihood:
AncestralStateTreeLikelihoodTest.java (+1 -1)
-
rambaut
2010-06-01 20:52
#3
Rev.: 3206
-
108 lines of code changed in 2 files:
-
src/dr/app/beagle/evomodel/parsers:
GeneralSubstitutionModelParser.java (+107 -43)
-
src/dr/evomodelxml/substmodel:
GeneralSubstitutionModelParser.java (+1 -2)
-
dong.w.xie
2010-06-01 15:22
#2
Rev.: 3205
-
23 lines of code changed in 2 files:
-
src/dr/app/tracer/application:
TracerFrame.java (+23)
-
src/dr/app/tracer/traces:
FilterDialog.java (-7)
-
dong.w.xie
2010-06-01 13:01
#1
Rev.: 3204
-
2873 lines of code changed in 52 files:
-
src/dr/app/coalgen:
CoalGenFrame.java (+1 -1)
-
src/dr/app/pathogen:
TreesPanel.java (+2 -2)
-
src/dr/app/tools:
SkylineReconstructor.java (+6 -9),
TimeSlicer.java (+13 -5)
-
src/dr/app/tracer/analysis:
BayesFactorsDialog.java (+9 -7),
BayesianSkylineDialog.java (+6 -5),
DemographicDialog.java (+3 -2),
GMRFSkyrideDialog.java (+4 -3),
LineagesThroughTimeDialog.java (+2 -1),
TimeDensityDialog.java (+2 -1),
TraitThroughTimeDialog.java (+2 -1)
-
src/dr/app/tracer/application:
TracerDefaultFileMenuFactory.java (+3 -1),
TracerFrame.java (+261 -46),
TracerMacFileMenuFactory.java (+4 -2)
-
src/dr/app/tracer/traces:
CombinedTraces.java (+45 -17),
CorrelationPanel.java (+315 -25),
DensityPanel.java (+115 -29),
FilterDialog.java (+245),
FrequencyPanel.java (+83 -20),
JIntervalsChart.java (+92 -80),
JTraceChart.java (+2 -2),
RawTracePanel.java (+71 -16),
SummaryStatisticsPanel.java (+91 -28),
TableScrollPane.java (+165),
TracePanel.java (+1 -1)
-
src/dr/gui/chart:
Axis.java (+13),
CategoryDensityPlot.java (new 188),
ChartLayout.java (+1 -1),
DensityPlot.java (del),
DiscreteJChart.java (new 111),
FrequencyPlot.java (+78 -10),
NumericalDensityPlot.java (new 156)
-
src/dr/inference/loggers:
ArrayLogFormatter.java (+3 -1)
-
src/dr/inference/trace:
AbstractTraceList.java (+6 -7),
ArrayTraceList.java (+8 -8),
DensityRectangle.java (+1 -1),
DnDsPerSiteAnalysis.java (+6 -6),
Filter.java (+70),
FilteredTraceList.java (+53),
LogFileTraces.java (+153 -43),
PathSamplingAnalysis.java (+4 -4),
Trace.java (+123 -57),
TraceAnalysis.java (+10 -4),
TraceCorrelation.java (+44 -3),
TraceDistribution.java (+224 -25),
TraceFactory.java (+57),
TraceList.java (+6 -3)
-
src/dr/inferencexml/trace:
MarginalLikelihoodAnalysisParser.java (+3 -2)
-
src/dr/util:
FrequencyDistribution.java (new)