-
rambaut
2008-08-30 20:49
#81
Rev.: 1172
-
133 lines of code changed in 3 files:
-
build_release.xml (+2)
-
src/dr/app/seqgen:
SeqGen.java (+66 -19)
-
src/dr/app/tools:
SpliceBeastFiles.java (+65)
-
rambaut
2008-08-30 07:27
#80
Rev.: 1171
-
5 lines of code changed in 2 files:
-
tracer_release.xml (+2 -1)
-
src/dr/evomodel/treelikelihood:
SequenceErrorModel.java (+3 -3)
-
rambaut
2008-08-29 06:06
#79
Rev.: 1170
-
275 lines of code changed in 5 files:
-
src/dr/app/beauti:
CreateModelDialog.java (del)
-
src/dr/app/seqgen:
SeqGen.java (+215)
-
src/dr/evomodel/sitemodel:
GammaSiteModel.java (+33 -2)
-
src/dr/evomodel/substmodel:
FrequencyModel.java (+18 -1),
HKY.java (+9)
-
alexander.alekseyenko
2008-08-23 05:03
#78
Rev.: 1169
-
139 lines of code changed in 7 files:
-
examples:
testBinary.xml (+14 -16)
-
src/dr/app/beast:
BeastParser.java (+1 -2)
-
src/dr/evomodel/MSSD:
CTMCScalePrior.java (+114),
alsDefaultPrior.java (del),
alsGammaPrior.java (del),
alsPriorLambdaIntegrator.java (del)
-
src/dr/evoxml:
NewickParser.java (+10)
-
alexei.drummond
2008-08-23 02:27
#77
Rev.: 1168
-
363 lines of code changed in 7 files:
-
examples/treePriors:
testYule.xml (+8 -8)
-
src/dr/app/beast:
BeastParser.java (+3 -4)
-
src/dr/evomodel/MSSD:
ALSTreeLikelihood.java (+63 -51),
AbstractObservationProcess.java (+78 -67),
ExponentialBranchLengthTreePrior.java (+164),
alsPriorLambdaIntegrator.java (new 47)
-
alexander.alekseyenko
2008-08-23 00:32
#76
Rev.: 1167
-
232 lines of code changed in 6 files:
-
examples:
testBinary.xml (+2 -2)
-
src/dr/app/beast:
BeastParser.java (+1)
-
src/dr/evomodel/MSSD:
AbstractObservationProcess.java (+4),
AnyTipObservationProcess.java (+2 -13),
SingleTipObservationProcess.java (+1 -1),
alsGammaPrior.java (new 222)
-
alexander.alekseyenko
2008-08-22 22:32
#75
Rev.: 1166
-
0 lines of code changed in 6 files:
-
src/dr/evomodel/alternativesplicing:
ImmigrationIntegrationForAlternativeSplicingPrior.java (del),
alsDefaultPrior.java (del),
alsPriorLambdaIntegrator.java (del)
-
src/dr/evomodel/treelikelihood:
AbstractObservationProcess.java (del),
AnyTipObservationProcess.java (del),
SingleTipObservationProcess.java (del)
-
alexei.drummond
2008-08-22 20:52
#74
Rev.: 1165
-
117 lines of code changed in 6 files:
-
src/dr/app/beast:
BeastParser.java (+5 -7)
-
src/dr/evolution/alignment:
AscertainedSitePatterns.java (+53 -45)
-
src/dr/evomodel/tree/randomlocalmodel:
RLTVAnalyzer.java (+54 -11),
RLTVLogger.java (-2)
-
src/dr/evomodel/treelikelihood:
ALSTreeLikelihood.java (del)
-
src/dr/evoxml:
AscertainedSitePatternsParser.java (+5 -7)
-
alexei.drummond
2008-08-21 08:45
#73
Rev.: 1164
-
111 lines of code changed in 3 files:
-
src/dr/evomodel/branchratemodel:
RandomLocalClockModel.java (+97 -54)
-
src/dr/evomodel/speciation:
RandomLocalYuleModel.java (+3 -2)
-
src/dr/inference/operators:
BitMoveOperator.java (+11 -1)
-
alexei.drummond
2008-08-21 07:09
#72
Rev.: 1163
-
38 lines of code changed in 11 files:
-
src/dr/evomodel/operators:
TreeBitRandomWalkOperator.java (+30 -15)
-
src/dr/evomodel/speciation:
RandomLocalYuleModel.java (-1)
-
src/dr/inference/model:
CompoundParameter.java (-1)
-
src/dr/inference/operators:
BitFlipOperator.java (+1 -2),
BitMoveOperator.java (-1),
CenteredScaleOperator.java (-16),
DeltaExchangeOperator.java (-16),
ScaleOperator.java (-16),
SimpleMCMCOperator.java (+5 -5),
UniformOperator.java (+1 -17)
-
src/test/dr/evomodel/speciation:
RLYModelTest.java (+1 -1)
-
bloomquist
2008-08-21 05:57
#71
Rev.: 1162
-
836 lines of code changed in 9 files:
-
src/dr/app/beast:
BeastParser.java (+2 -2)
-
src/dr/evomodel/coalescent:
AbstractFixedGridLogger.java (+106),
BayesianSkylineFixedGridLogger.java (+183),
GMRFFixedGridImportanceSampler.java (+97),
GMRFSkyrideFixedGridLogger.java (+448)
-
src/dr/evomodel/tree:
AbstractFixedGridLogger.java (del),
BayesianSkylineFixedGridLogger.java (del),
GMRFFixedGridImportanceSampler.java (del),
GMRFSkyrideFixedGridLogger.java (del)
-
alexei.drummond
2008-08-21 02:55
#70
Rev.: 1161
-
111 lines of code changed in 2 files:
-
src/dr/evomodel/speciation:
RandomLocalYuleModel.java (+84 -48),
SpeciationModel.java (+27 -22)
-
alexei.drummond
2008-08-21 01:05
#69
Rev.: 1160
-
24 lines of code changed in 3 files:
-
src/dr/evomodel/speciation:
RandomLocalYuleModel.java (+14 -24)
-
src/dr/evomodel/tree:
TreeModel.java (+4 -2)
-
src/dr/inference/model:
CompoundParameter.java (+6 -1)
-
alexei.drummond
2008-08-20 23:31
#68
Rev.: 1159
-
608 lines of code changed in 10 files:
-
src/dr/app/beast:
BeastParser.java (+3 -2)
-
src/dr/evomodel/branchratemodel:
RandomLocalClockModel.java (+24 -8)
-
src/dr/evomodel/randomYule:
RandomLocalYuleModel.java (del),
RandomYuleAnalyzer.java (del),
RandomYuleLogger.java (del)
-
src/dr/evomodel/speciation:
RandomLocalYuleModel.java (+222)
-
src/dr/evomodel/tree/randomlocalmodel:
RLTVAnalyzer.java (+201),
RLTVLogger.java (+128),
RandomLocalTreeVariable.java (+29)
-
src/test/dr/evomodel/speciation:
RLYModelTest.java (+1 -1)
-
alexei.drummond
2008-08-20 09:32
#67
Rev.: 1158
-
201 lines of code changed in 3 files:
-
src/dr/evomodel/randomYule:
RandomLocalYuleModel.java (new),
RandomYuleAnalyzer.java (new 201)
-
alexei.drummond
2008-08-20 05:20
#66
Rev.: 1157
-
344 lines of code changed in 5 files:
-
src/dr/app/beast:
BeastParser.java (+4 -1)
-
src/dr/evomodel/randomYule:
RandomLocalYuleModel.java (+215),
RandomYuleLogger.java (new 124)
-
src/dr/evomodel/speciation:
RandomLocalYuleModel.java (del)
-
src/test/dr/evomodel/speciation:
RLYModelTest.java (+1 -1)
-
alexei.drummond
2008-08-19 22:53
#65
Rev.: 1156
-
1086 lines of code changed in 12 files:
-
src/dr/app/beast:
BeastParser.java (+289 -287)
-
src/dr/evolution/tree:
Tree.java (+1 -1)
-
src/dr/evomodel/operators:
TreeBitMoveOperator.java (+41 -12),
TreeBitRandomWalkOperator.java (+168)
-
src/dr/evomodel/speciation:
RandomLocalYuleModel.java (new 234)
-
src/dr/evomodel/tree:
TreeModel.java (+8)
-
src/dr/inference/mcmc:
MCMC.java (+49 -27)
-
src/dr/inference/trace:
LogFileTraces.java (+15 -8),
TracesListener.java (new 11),
TracesReader.java (new 122)
-
src/dr/util:
FileHelpers.java (+5 -6)
-
src/test/dr/evomodel/speciation:
RLYModelTest.java (+143)
-
bloomquist
2008-08-19 10:11
#64
Rev.: 1155
-
92 lines of code changed in 2 files:
-
src/dr/app/beast:
BeastParser.java (+2 -1)
-
src/dr/inference/model:
SubStatistic.java (+90)
-
msuchard
2008-08-18 06:41
#63
Rev.: 1154
-
55 lines of code changed in 3 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+15 -1)
-
src/dr/app/beauti/options:
BeautiOptions.java (+4)
-
src/dr/evomodel/coalescent:
GMRFSkyrideLikelihood.java (+36 -40)
-
alexei.drummond
2008-08-17 23:55
#62
Rev.: 1153
-
344 lines of code changed in 5 files:
-
src/dr/evolution/tree:
Tree.java (+86 -44)
-
src/dr/evomodel/arg:
OldTreeLogger.java (+223 -223)
-
src/dr/evomodel/tree:
TreeLogger.java (+17 -6)
-
src/dr/evomodelxml:
TreeLoggerParser.java (+17 -4)
-
src/test/dr/evomodel/operators:
ExchangeOperatorTest.java (+1 -1)
-
msuchard
2008-08-17 15:02
#61
Rev.: 1152
-
3618 lines of code changed in 10 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+1124 -1103),
Generator.java (+140 -135),
TreePriorGenerator.java (+493 -454)
-
src/dr/app/beauti/options:
BeautiOptions.java (+914 -895),
ModelOptions.java (+94 -91),
OperatorType.java (+27 -26),
Parameter.java (+154 -153),
TreePrior.java (+16 -15)
-
src/dr/app/beauti/priorsPanel:
PriorDialog.java (+318 -312)
-
src/dr/app/beauti/treespanel:
TreesPanel.java (+338 -325)
-
rambaut
2008-08-17 08:39
#60
Rev.: 1151
-
494 lines of code changed in 7 files:
-
src/dr/app/beauti/modelsPanel:
CreateModelDialog.java (+111),
ModelsPanel.java (+1 -1)
-
src/dr/app/beauti/treespanel:
CreateTreeDialog.java (+120),
TreeDisplayPanel.java (+8 -1),
TreesPanel.java (+166 -103),
UserTreePanel.java (del)
-
src/dr/app/tools:
TemporalRooting.java (+88)
-
alexei.drummond
2008-08-17 08:03
#59
Rev.: 1150
-
330 lines of code changed in 4 files:
-
src/dr/evomodel/tree:
TreeSummary.java (+254)
-
src/dr/inference/loggers:
LogColumn.java (new),
TreeLogger.java (del)
-
bloomquist
2008-08-17 07:30
#58
Rev.: 1149
-
102 lines of code changed in 2 files:
-
src/dr/evomodel/coalescent:
GMRFSkyrideLikelihood.java (+8 -3)
-
src/dr/evomodel/tree:
GMRFSkyrideFixedGridLogger.java (new 94)
-
bloomquist
2008-08-17 06:33
#57
Rev.: 1148
-
68 lines of code changed in 2 files:
-
src/dr/evomodel/coalescent:
GMRFSkyrideLikelihood.java (+8 -3)
-
src/dr/evomodel/tree:
GMRFSkyrideFixedGridLogger.java (+60 -8)
-
rambaut
2008-08-17 00:56
#56
Rev.: 1147
-
294 lines of code changed in 2 files:
-
src/dr/app/beauti/treespanel:
TreeDisplayPanel.java (+99),
TreesPanel.java (+195 -25)
-
rambaut
2008-08-16 23:52
#55
Rev.: 1146
-
183 lines of code changed in 7 files:
-
src/dr/app/beauti:
BeautiFrame.java (+54 -14)
-
src/dr/app/beauti/treespanel:
TreesPanel.java (+20 -6)
-
src/dr/app/tools:
BeastOptions.java (del),
NexusApplicationImporter.java (del),
NexusConverter.java (del),
XMLWriter.java (del)
-
src/dr/evomodel/tree:
GMRFSkyrideFixedGridLogger.java (+109 -108)
-
bloomquist
2008-08-16 16:13
#54
Rev.: 1145
-
1 lines of code changed in 1 file:
-
src/dr/evomodel/coalescent:
GMRFSkyrideLikelihood.java (+1 -1)
-
bloomquist
2008-08-16 11:50
#53
Rev.: 1144
-
1 lines of code changed in 1 file:
-
src/dr/inference/operators:
SimpleOperatorSchedule.java (+1 -1)
-
bloomquist
2008-08-16 11:23
#52
Rev.: 1143
-
58 lines of code changed in 3 files:
-
src/dr/evomodel/coalescent:
CovariateGMRFSkylineLikelihood.java (+1 -1),
GMRFSkyrideLikelihood.java (+56 -9),
GMRFTestLikelihood.java (+1 -1)
-
rambaut
2008-08-16 10:58
#51
Rev.: 1142
-
80 lines of code changed in 7 files:
-
src/dr/app/beauti:
BeautiFrame.java (+6 -5),
DiscretePriorDialog.java (del)
-
src/dr/app/beauti/treespanel:
TreesPanel.java (+15 -2),
UserTreePanel.java (new 17)
-
src/dr/evolution/tree:
FlexibleTree.java (+5 -1)
-
src/dr/gui/chart:
JChart.java (+3 -3),
RegressionPlot.java (+34 -26)
-
bloomquist
2008-08-16 09:22
#50
Rev.: 1141
-
690 lines of code changed in 6 files:
-
src/dr/app/beast:
BeastParser.java (+3)
-
src/dr/evomodel/coalescent:
CoalescentIntervalStatistic.java (+58),
LineageCountStatistic.java (+55)
-
src/dr/evomodel/tree:
AbstractFixedGridLogger.java (new 106),
BayesianSkylineFixedGridLogger.java (new 184),
GMRFSkyrideFixedGridLogger.java (+284 -147)
-
msuchard
2008-08-16 08:23
#49
Rev.: 1140
-
19 lines of code changed in 2 files:
-
src/dr/math/distributions:
PoissonDistribution.java (+12)
-
src/test/dr/evomodel/arg/operators:
ARGAddRemoveOperatorTest.java (+7 -5)
-
alexei.drummond
2008-08-16 02:58
#48
Rev.: 1139
-
31 lines of code changed in 2 files:
-
src/dr/evomodel/operators:
ExchangeOperator.java (+1 -1)
-
src/test/dr/evomodel/operators:
ExchangeOperatorTest.java (+30 -32)
-
Sebastian.Hoehna
2008-08-15 18:44
#47
Rev.: 1138
-
1630 lines of code changed in 10 files:
-
src/dr/evomodel/operators:
AbstractTreeOperator.java (-32),
FNPR.java (+41 -49),
GibbsPruneAndRegraft.java (+239),
GibbsSubtreeSwap.java (+295),
ImportancePruneAndRegraft.java (+363),
ImportanceSubtreeSwap.java (+383),
NNI.java (+23 -28),
SimpleGibbsOperator.java (+161),
SimpleOperator.java (+124)
-
src/dr/inference/loggers:
ConvergenceLogger.java (+1 -2)
-
Sebastian.Hoehna
2008-08-15 18:42
#46
Rev.: 1137
-
402 lines of code changed in 3 files:
-
src/test/dr/evomodel/operators:
FNPRTest.java (+127),
ImportancesubtreeSwapTest.java (new 165),
NNITest.java (+110)
-
Sebastian.Hoehna
2008-08-15 12:44
#45
Rev.: 1136
-
64 lines of code changed in 1 file:
-
src/test/dr/evomodel/operators:
ExchangeOperatorTest.java (+64 -6)
-
msuchard
2008-08-15 12:42
#44
Rev.: 1135
-
283 lines of code changed in 5 files:
-
src/dr/app/beast:
BeastParser.java (+2 -1)
-
src/dr/evomodel/arg:
ARGModel.java (+5 -5),
ARGReassortmentNodeCountStatistic.java (new 68)
-
src/dr/evomodel/arg/coalescent:
ARGUniformPrior.java (+1 -1)
-
src/test/dr/evomodel/arg/operators:
ARGAddRemoveOperatorTest.java (+207)
-
Sebastian.Hoehna
2008-08-15 11:50
#43
Rev.: 1134
-
1209 lines of code changed in 3 files:
-
src/dr/inference/loggers:
ConvergenceListener.java (+271),
ConvergenceLogger.java (+405),
TreeLogger.java (new 533)
-
rambaut
2008-08-15 11:08
#42
Rev.: 1133
-
1840 lines of code changed in 18 files:
-
src/dr/app/beauti:
BeautiFrame.java (+71 -49),
BeautiTester.java (+1 -2),
NexusApplicationImporter.java (new 421),
SamplesPanel.java (+11 -84)
-
src/dr/app/beauti/generator:
InitialTreeGenerator.java (+85 -74),
TreeModelGenerator.java (+4 -5)
-
src/dr/app/beauti/options:
BeautiOptions.java (+4 -5),
StartingTreeType.java (+25)
-
src/dr/app/beauti/priorsPanel:
DiscretePriorDialog.java (+148),
PriorsPanel.java (+1 -141)
-
src/dr/app/beauti/treespanel:
TreesPanel.java (+232),
UserTreePanel.java (+85)
-
src/dr/app/tools:
RootToTip.java (+285),
TemporalRooting.java (+224)
-
src/dr/evolution/io:
NexusImporter.java (+1 -1)
-
src/dr/evolution/tree:
FlexibleTree.java (+39 -54),
Tree.java (+29)
-
src/dr/stats:
Regression.java (+174 -166)
-
msuchard
2008-08-15 04:05
#41
Rev.: 1131
-
6 lines of code changed in 2 files:
-
src/dr/app/beast:
BeastParser.java (+1 -1)
-
src/dr/evomodel/continuous:
MultivariateTraitLikelihood.java (+5)
-
alexei.drummond
2008-08-15 03:44
#40
Rev.: 1130
-
198 lines of code changed in 5 files:
-
src/dr/app/tracer/analysis:
DemographicDialog.java (+35 -48)
-
src/dr/evomodel/tree:
TreeLogger.java (+7 -1)
-
src/dr/inference/operators:
ScaleOperator.java (+6)
-
src/test/dr/evomodel/operators:
ExchangeOperatorTest.java (+127 -9)
-
src/test/dr/evomodel/speciation:
YuleModelTest.java (+23 -10)
-
Sebastian.Hoehna
2008-08-14 14:35
#39
Rev.: 1129
-
0 lines of code changed in 2 files:
-
src/dr/inference/markovchain:
ConvergenceListener.java (del),
ConvergenceListenerParser.java (del)
-
Sebastian.Hoehna
2008-08-14 14:27
#38
Rev.: 1128
-
627 lines of code changed in 2 files:
-
src/dr/evolution/tree:
ConditionalCladeFrequency.java (+476),
ConditionalCladeFrequencyParser.java (new 151)
-
Sebastian.Hoehna
2008-08-14 14:25
#37
Rev.: 1127
-
10 lines of code changed in 1 file:
-
src/dr/evolution/tree:
Clade.java (+10 -5)
-
msuchard
2008-08-14 11:09
#36
Rev.: 1126
-
15969 lines of code changed in 33 files:
-
src/dr/app/beast:
BeastParser.java (+286 -266)
-
src/dr/evomodel/arg:
ARGLogger.java (+247),
ARGModel.java (+4416),
ARGTrace.java (new 191),
ARGTraceAnalysis.java (+323),
ARGTraceAnalysisParser.java (new 85),
ARGTree.java (+828),
ARGTreeLogger.java (new 249),
OldTreeLogger.java (+341),
UniformPartitionLikelihood.java (+121)
-
src/dr/evomodel/arg/branchratemodel:
ARGDiscretizedBranchRates.java (+307)
-
src/dr/evomodel/arg/coalescent:
ARGCoalescentLikelihood.java (+310),
ARGUniformPrior.java (+422),
VeryOldCoalescentLikelihood.java (+684)
-
src/dr/evomodel/arg/likelihood:
ARGLikelihood.java (+560),
AbstractARGLikelihood.java (+337)
-
src/dr/evomodel/arg/operators:
ARGAddRemoveEventOperator.java (+1153),
ARGExchangeOperator.java (+413),
ARGPartitioningOperator.java (+234),
ARGReassortmentOperator.java (+129),
ARGSubtreeSlideOperator.java (+616),
ARGSwapOperator.java (+605),
NonContiguousPartitionsException.java (new 14),
ObsoleteARGAddRemoveEventOperator.java (+1042),
ObsoleteARGNewEventOperator.java (+731),
SlidingPatternsOperator.java (+306)
-
src/dr/evomodel/treelikelihood:
NativeCovarionLikelihoodCore.java (new 114)
-
src/dr/evoxml:
GraphMLUtils.java (new 228)
-
src/dr/inference/model:
ARGCompoundParameter.java (+275),
VariableSizeCompoundParameter.java (+141),
VariableSizeParameter.java (new 193)
-
src/dr/math:
MathUtils.java (+32),
MersenneTwisterFast.java (+36 -4)
-
alexei.drummond
2008-08-14 09:28
#35
Rev.: 1125
-
197 lines of code changed in 3 files:
-
src/dr/app/beast:
BeastRemote.java (+99 -103)
-
src/test/dr/evomodel/operators:
ExchangeOperatorTest.java (+90)
-
src/test/dr/evomodel/speciation:
YuleModelTest.java (+8 -10)
-
bloomquist
2008-08-13 07:27
#34
Rev.: 1118
-
64 lines of code changed in 2 files:
-
src/dr/evolution/util:
RandomTaxaSample.java (+57 -2)
-
src/dr/math:
Binomial.java (+7 -1)
-
msuchard
2008-08-13 07:04
#33
Rev.: 1117
-
1562 lines of code changed in 12 files:
-
build_release.xml (+147 -147)
-
lib:
mpj.jar (new)
-
src/dr/app/beast:
BeastRemote.java (+175)
-
src/dr/inference/model:
AbstractModel.java (+177 -119),
CompoundLikelihood.java (+184 -184),
ParallelCompoundLikelihood.java (+162),
ParallelLikelihood.java (new 13),
Parameter.java (+383 -364)
-
src/dr/inference/parallel:
MPILikelihoodRunner.java (+183),
MPISerializable.java (new 12),
MPIServices.java (+86),
ServiceRequest.java (new 40)
-
msuchard
2008-08-13 04:22
#32
Rev.: 1115
-
8 lines of code changed in 1 file:
-
src/dr/inference/distribution:
MultivariateDistributionLikelihood.java (+8 -8)
-
rambaut
2008-08-12 23:00
#31
Rev.: 1114
-
0 lines of code changed in 1 file:
-
rambaut
2008-08-12 22:55
#30
Rev.: 1113
-
14 lines of code changed in 2 files:
-
src/dr/app/tracer/application:
TracerApp.java (+14 -16)
-
src/dr/evomodel/treelikelihood:
ADNADamageModel.java (del)
-
alexei.drummond
2008-08-12 21:16
#29
Rev.: 1112
-
4911 lines of code changed in 76 files:
-
src/dr/app/beauti/priorsPanel:
PriorDialog.java (+1 -1),
PriorOptionsPanel.java (+1 -1)
-
src/dr/evolution/wrightfisher:
CodonFitnessFunction.java (+113 -113),
GammaFitnessFunction.java (+65 -65),
GammaInvFitnessFunction.java (new)
-
src/dr/evomodel/clock:
ACLikelihood.java (+1 -1),
EDLikelihood.java (+2 -2),
GDLikelihood.java (+2 -2),
NDLikelihood.java (+1 -1)
-
src/dr/evomodel/coalescent/operators:
BayesianSkylineGibbsOperator.java (+4 -3),
GMRFSkyrideFixedEffectsGibbsOperator.java (+2 -2)
-
src/dr/evomodel/continuous:
MultivariateDiffusionModel.java (+109 -109),
MultivariateTDiffusionModel.java (+71 -71)
-
src/dr/evomodel/operators:
InternalTraitGibbsOperator.java (+1 -1),
PrecisionMatrixGibbsOperator.java (+123 -124)
-
src/dr/evomodel/sitemodel:
GammaSiteModel.java (+87 -49)
-
src/dr/gui/chart:
PDFPlot.java (+6 -6)
-
src/dr/inference/distribution:
DistributionLikelihood.java (+343 -343),
ExponentialDistributionModel.java (+1 -1),
ExponentialMarkovModel.java (+3 -2),
GammaDistributionModel.java (+181 -141),
LogNormalDistributionModel.java (+1 -1),
MultivariateDistributionLikelihood.java (+9 -9),
MultivariateOUModel.java (+328 -328),
NormalDistributionModel.java (+169 -169),
ParametricDistributionModel.java (new),
UniformDistributionModel.java (+1 -1)
-
src/dr/inference/model:
OrnsteinUhlenbeckPriorLikelihood.java (+1 -1)
-
src/dr/inference/operators:
MVOUCovarianceOperator.java (+1 -1),
RegressionGibbsOperator.java (new 124)
-
src/dr/inference/prior:
GammaParameterPrior.java (+40 -34),
NormalParameterPrior.java (+40 -34)
-
src/dr/math:
BoundsCheckedFunction.java (+54 -66),
ChiSquareDistribution.java (del),
DirichletDistribution.java (del),
Distribution.java (del),
ExponentialDistribution.java (del),
GammaDistribution.java (del),
InverseWishartDistribution.java (del),
LaplaceDistribution.java (del),
LogNormalDistribution.java (del),
MultivariateDistribution.java (del),
MultivariateGammaDistribution.java (del),
MultivariateNormalDistribution.java (del),
NormalDistribution.java (del),
OffsetPositiveDistribution.java (del),
PoissonDistribution.java (del),
RiemannApproximation.java (new),
TDistribution.java (del),
TruncatedNormalDistribution.java (del),
UniformDistribution.java (del),
WishartDistribution.java (del)
-
src/dr/math/distributions:
ChiSquareDistribution.java (new 129),
DirichletDistribution.java (+61),
Distribution.java (new 89),
ExponentialDistribution.java (new 167),
GammaDistribution.java (+719),
InverseWishartDistribution.java (+110),
LaplaceDistribution.java (+111),
LogNormalDistribution.java (+200),
MultivariateDistribution.java (+20),
MultivariateGammaDistribution.java (new 54),
MultivariateNormalDistribution.java (+138),
NormalDistribution.java (+190),
OffsetPositiveDistribution.java (+110),
PoissonDistribution.java (+61),
TDistribution.java (new 87),
TruncatedNormalDistribution.java (+234),
UniformDistribution.java (+172),
WishartDistribution.java (+253)
-
alexei.drummond
2008-08-12 20:52
#28
Rev.: 1111
-
2 lines of code changed in 1 file:
-
src/dr/app/beauti/priorsPanel:
PriorDialog.java (+2 -37)
-
alexei.drummond
2008-08-12 20:47
#27
Rev.: 1110
-
584 lines of code changed in 8 files:
-
src/dr/app/beauti/options:
Parameter.java (+2)
-
src/dr/app/beauti/priorsPanel:
PriorDialog.java (+176 -117),
PriorOptionsPanel.java (+74),
PriorType.java (+8)
-
src/dr/math:
ExponentialDistribution.java (new 117),
LaplaceDistribution.java (new 4),
OffsetPositiveDistribution.java (new 108),
UniformDistribution.java (new 95)
-
alexei.drummond
2008-08-12 09:01
#26
Rev.: 1109
-
818 lines of code changed in 6 files:
-
src/dr/app/beauti:
BeautiFrame.java (+2 -1),
ModelsPanel.java (del)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+10 -1)
-
src/dr/app/beauti/modelsPanel:
ModelsPanel.java (+459),
PartitionModelPanel.java (+345)
-
src/dr/app/beauti/options:
PartitionModel.java (+2)
-
rambaut
2008-08-09 20:40
#25
Rev.: 1103
-
1 lines of code changed in 1 file:
-
tracer_release.xml (+1 -1)
-
rambaut
2008-08-09 20:39
#24
Rev.: 1102
-
0 lines of code changed in 1 file:
-
jen.tom
2008-08-09 10:44
#23
Rev.: 1101
-
4 lines of code changed in 1 file:
-
src/dr/inference/operators:
SimpleOperatorSchedule.java (+4 -1)
-
bloomquist
2008-08-09 10:41
#22
Rev.: 1100
-
2 lines of code changed in 1 file:
-
src/dr/evomodel/tree:
GMRFSkyrideFixedGridLogger.java (+2 -2)
-
rambaut
2008-08-09 02:41
#21
Rev.: 1099
-
213 lines of code changed in 4 files:
-
src/dr/app/beast:
BeastParser.java (+2 -1)
-
src/dr/app/tracer/analysis:
TemporalAnalysisPlotPanel.java (+2 -2)
-
src/dr/app/tracer/application:
TracerApp.java (+5 -5)
-
src/dr/evomodel/treelikelihood:
SequenceErrorModel.java (+204)
-
rambaut
2008-08-08 12:12
#20
Rev.: 1098
-
373 lines of code changed in 11 files:
-
src/dr/app/tracer/analysis:
BayesFactorsDialog.java (+9 -9),
BayesianSkylineDialog.java (+4 -1),
DemographicDialog.java (+30 -9),
TemporalAnalysisPlotPanel.java (+15 -14),
TimeDensityDialog.java (+246)
-
src/dr/app/tracer/application:
AnalysisMenuFactory.java (+14 -14),
TableSorter.java (del),
TracerApp.java (+32 -27),
TracerFrame.java (+19 -4),
TracerMenuHandler.java (del)
-
src/dr/gui/chart:
JChart.java (+4 -1)
-
rambaut
2008-08-08 04:14
#19
Rev.: 1097
-
377 lines of code changed in 10 files:
-
examples:
anolis.nex (new 37),
testGeneralSubstitutionModel.xml (+184 -184)
-
src/dr/app/tracer/application:
TracerFrame.java (+5 -3)
-
src/dr/app/tracer/traces:
SummaryStatisticsPanel.java (+3 -3)
-
src/dr/gui/chart:
Axis.java (+13 -18),
JChart.java (+5 -5),
LogAxis.java (+2 -2)
-
src/dr/stats:
DiscreteStatistics.java (+27 -15)
-
src/dr/util:
NumberFormatter.java (+101 -102)
-
rambaut
2008-08-07 23:45
#18
Rev.: 1096
-
2 lines of code changed in 1 file:
-
src/dr/app/beast:
BeastVersion.java (+2 -2)
-
rambaut
2008-08-07 23:42
#17
Rev.: 1095
-
2 lines of code changed in 1 file:
-
src/dr/app/beauti:
NexusApplicationImporter.java (+2 -4)
-
alexei.drummond
2008-08-07 23:18
#16
Rev.: 1094
-
25 lines of code changed in 1 file:
-
src/dr/app/beauti:
NexusApplicationImporter.java (+25 -3)
-
alexei.drummond
2008-08-07 12:40
#15
Rev.: 1093
-
46 lines of code changed in 1 file:
-
src/dr/app/tools:
TreeAnnotator.java (+46 -1)
-
alexei.drummond
2008-08-07 12:04
#14
Rev.: 1092
-
858 lines of code changed in 1 file:
-
src/dr/app/tools:
TreeAnnotator.java (+858 -849)
-
alexei.drummond
2008-08-07 08:33
#13
Rev.: 1091
-
1145 lines of code changed in 15 files:
-
src/dr/app/beauti:
BeautiFrame.java (+1),
DiscretePriorDialog.java (new 96),
PriorDialog.java (del),
PriorType.java (del),
PriorsPanel.java (del)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+2 -2),
Generator.java (+1 -1),
InitialTreeGenerator.java (+1 -1)
-
src/dr/app/beauti/options:
BeautiOptions.java (+4 -1),
ModelOptions.java (+1 -1),
Parameter.java (+2 -2)
-
src/dr/app/beauti/priorsPanel:
PriorDialog.java (+423),
PriorTableModel.java (+78),
PriorType.java (+127),
PriorsPanel.java (+409)
-
alexei.drummond
2008-08-07 08:09
#12
Rev.: 1090
-
178 lines of code changed in 6 files:
-
src/dr/app/beast:
BeastParser.java (+2 -1)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+3 -3),
BranchRatesModelGenerator.java (+15 -9),
TreeLikelihoodGenerator.java (+12 -9)
-
src/dr/evomodel/branchratemodel:
DiscretizedBranchRates.java (+63 -66)
-
src/dr/evomodelxml:
DiscretizedBranchRatesParser.java (+83)
-
alexei.drummond
2008-08-07 05:32
#11
Rev.: 1089
-
0 lines of code changed in 2 files:
-
src/dr/gui/table/images:
sortAscending.png (new),
sortDescending.png (new)
-
alexei.drummond
2008-08-06 14:24
#10
Rev.: 1088
-
15 lines of code changed in 4 files:
-
src/dr/app/beauti:
BeautiFrame.java (+1 -1),
BeautiTester.java (+1 -1)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+3 -1)
-
src/dr/app/beauti/options:
DataPartition.java (+10 -3)
-
alexei.drummond
2008-08-06 13:38
#9
Rev.: 1087
-
9 lines of code changed in 3 files:
-
build_release.xml (+1)
-
src/dr/evolution/tree:
Tree.java (+2 -2)
-
src/dr/evomodel/tree:
TMRCAStatistic.java (+6 -3)
-
alexei.drummond
2008-08-06 08:48
#8
Rev.: 1086
-
139 lines of code changed in 2 files:
-
src/dr/inference/operators:
RandomWalkOperator.java (+19 -30)
-
src/dr/xml:
StringAttributeRule.java (+120 -104)
-
alexei.drummond
2008-08-06 06:39
#7
Rev.: 1085
-
581 lines of code changed in 8 files:
-
examples/treePriors:
testCataclysmCoalescent.xml (+209)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+6 -1)
-
src/dr/evomodel/coalescent:
TwoEpochDemographicModel.java (+77 -75)
-
src/dr/evomodel/speciation:
SpeciationLikelihood.java (+22 -18)
-
src/dr/inference/operators:
RandomWalkOperator.java (+2 -4)
-
src/dr/math:
LaplaceDistribution.java (+100)
-
src/test/dr/evomodel/speciation:
YuleModelTest.java (+133)
-
src/test/dr/inference:
TraceTest.java (new 32)
-
rambaut
2008-08-06 03:06
#6
Rev.: 1084
-
53 lines of code changed in 1 file:
-
src/dr/inference/operators:
RandomWalkOperator.java (+53 -7)
-
rambaut
2008-08-06 02:48
#5
Rev.: 1083
-
224 lines of code changed in 11 files:
-
src/dr/evomodel/speciation:
SpeciationModel.java (+1 -1)
-
src/dr/evomodel/tree:
TreeModelParser.java (del)
-
src/dr/evomodel/treelikelihood:
ADNADamageModel.java (new 161),
AbstractLikelihoodCore.java (new),
ArbitraryPrecisionLikelihoodCore.java (new),
LikelihoodCore.java (+7),
TipPartialsModel.java (+6 -19),
TreeLikelihood.java (+23 -14)
-
msuchard
2008-08-05 11:24
#4
Rev.: 1082
-
187 lines of code changed in 4 files:
-
examples:
testComparativeMethod.xml (new 4)
-
src/dr/evomodel/operators:
PrecisionMatrixGibbsOperator.java (+13 -6)
-
src/dr/inference/distribution:
MultivariateDistributionLikelihood.java (+28 -8)
-
src/dr/math:
WishartDistribution.java (new 142)
-
rambaut
2008-08-05 01:16
#3
Rev.: 1080
-
1479 lines of code changed in 7 files:
-
src/dr/app/beast:
BeastParser.java (+2 -1)
-
src/dr/app/beauti/generator:
TreeModelGenerator.java (+1 -1)
-
src/dr/app/tools:
BeastOptions.java (new 1175)
-
src/dr/evomodel/branchratemodel:
RateEpochBranchRateModel.java (+1 -1)
-
src/dr/evomodel/speciation:
SpeciationLikelihood.java (+26 -2)
-
src/dr/evomodel/tree:
TreeModel.java (+4 -4)
-
src/dr/evomodelxml:
TreeModelParser.java (+270)
-
rambaut
2008-08-04 22:42
#2
Rev.: 1079
-
133 lines of code changed in 3 files:
-
build_release.xml (+1)
-
src/dr/evomodel/speciation:
SpeciationLikelihood.java (+36 -4),
SpeciationModel.java (+96 -36)
-
rambaut
2008-08-04 21:26
#1
Rev.: 1078
-
12 lines of code changed in 5 files:
-
src/dr/evolution/coalescent:
ExponentialLogistic.java (+3 -2),
LogisticGrowth.java (new)
-
src/dr/evomodel/coalescent:
ExponentialLogisticModel.java (+2 -6)