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rambaut
2012-08-20 21:05
#25
Rev.: 5148
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8 lines of code changed in 1 file:
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src/dr/evomodelxml/treelikelihood:
TreeTraitParserUtilities.java (+8 -7)
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rambaut
2012-08-18 21:54
#24
Rev.: 5145
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10 lines of code changed in 2 files:
-
src/dr/inference/markovchain:
MarkovChain.java (new)
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msuchard
2012-08-18 06:32
#23
Rev.: 5142
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2 lines of code changed in 1 file:
-
src/dr/app/beauti/components/dollo:
DolloComponentGenerator.java (+2 -2)
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rambaut
2012-08-18 02:36
#22
Rev.: 5141
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14 lines of code changed in 1 file:
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src/dr/inference/model:
CompoundLikelihood.java (+14 -14)
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rambaut
2012-08-18 02:25
#21
Rev.: 5139
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16 lines of code changed in 1 file:
-
src/dr/inference/markovchain:
MarkovChain.java (+16 -6)
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rambaut
2012-08-17 21:06
#20
Rev.: 5137
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14 lines of code changed in 2 files:
-
src/dr/inference/markovchain:
MarkovChain.java (+5)
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src/dr/inference/model:
CompoundLikelihood.java (+9 -7)
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rambaut
2012-08-16 03:27
#19
Rev.: 5136
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0 lines of code changed in 1 file:
-
src/dr/inference/mcmc:
MCMC.java (-8)
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rambaut
2012-08-15 22:34
#18
Rev.: 5133
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9 lines of code changed in 3 files:
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src/dr/app/beagle/evomodel/parsers:
TreeLikelihoodParser.java (+1 -1)
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src/dr/inference/model:
CompoundLikelihood.java (+4 -3)
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src/dr/inferencexml/model:
CompoundLikelihoodParser.java (+4 -4)
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dong.w.xie@gmail.com
2012-08-13 14:17
#17
Rev.: 5129
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51 lines of code changed in 8 files:
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src/dr/app/beauti/generator:
TreePriorGenerator.java (+5 -4)
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src/dr/app/beauti/options:
PartitionTreePrior.java (new)
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src/dr/evomodelxml/speciation:
BirthDeathSerialSamplingModelParser.java (+7 -4)
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src/test/dr/evomodel/speciation:
BirthDeathSSLikelihoodTest.java (new)
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msuchard
2012-08-12 12:03
#16
Rev.: 5124
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3 lines of code changed in 2 files:
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src/dr/app/beast:
BeastMain.java (+2 -1)
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src/dr/inferencexml/model:
CompoundLikelihoodParser.java (+1 -1)
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rambaut
2012-08-11 08:53
#15
Rev.: 5122
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35 lines of code changed in 5 files:
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src/dr/inference/loggers:
TreeLogger.java (del)
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src/dr/inference/mcmc:
MCMC.java (+8 -9)
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src/dr/inferencexml:
MCMCParser.java (+3 -1)
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src/dr/xml:
XMLParser.java (+24 -19)
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dong.w.xie@gmail.com
2012-08-10 13:05
#14
Rev.: 5121
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2 lines of code changed in 2 files:
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src/dr/evomodel/speciation:
BirthDeathSerialSamplingModel.java (+2 -2)
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danny.wilson@gmail.com
2012-08-09 04:56
#13
Rev.: 5119
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1454 lines of code changed in 9 files:
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src/dr/app/beast:
development_parsers.properties (+2)
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src/dr/evomodel/epidemiology:
LambertW.java (new 254),
LogisticGrowthN0.java (new 147),
LogisticGrowthN0Model.java (new 88),
LogisticGrowthN0ModelParser.java (new 80),
ODEDemographicFunction.java (new 397),
SIRepidemic.java (new 282),
SIRepidemicModel.java (new 117),
SIRepidemicModelParser.java (new 87)
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rambaut
2012-08-09 01:27
#12
Rev.: 5118
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2 lines of code changed in 2 files:
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src/dr/app/beagle/evomodel/parsers:
GammaSiteModelParser.java (+1 -1)
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src/dr/app/beauti/util:
BEAUTiImporter.java (+1 -1)
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rambaut
2012-08-08 23:06
#11
Rev.: 5116
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12 lines of code changed in 10 files:
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src/dr/evomodel/epidemiology:
DynamicalForce.java (+3),
DynamicalSystem.java (+3),
DynamicalVariable.java (new),
SIRModel.java (new),
SIRModelParser.java (+3)
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rambaut
2012-08-08 22:36
#10
Rev.: 5114
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3 lines of code changed in 2 files:
-
examples/release/testXML:
testBinaryDollo.xml (+3 -3)
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rambaut
2012-08-08 22:32
#9
Rev.: 5113
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176 lines of code changed in 6 files:
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src/dr/app/beagle/evomodel/parsers:
GammaSiteModelParser.java (+37 -42)
-
src/dr/app/beast:
release_parsers.properties (+1)
-
src/dr/app/beauti/components/dollo:
DolloComponentGenerator.java (+3 -2)
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src/dr/evomodelxml/MSSD:
ALSSiteModelParser.java (new 121)
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src/dr/evomodelxml/sitemodel:
GammaSiteModelParser.java (new)
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rambaut
2012-08-08 21:31
#8
Rev.: 5110
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83 lines of code changed in 7 files:
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release/common:
README.txt (+2 -2),
VERSION HISTORY.txt (+59 -4)
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src/dr/app/beauti:
BeautiFrame.java (+10 -27)
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src/dr/app/beauti/mcmcpanel:
MCMCPanel.java (+8 -8)
-
src/dr/app/beauti/options:
BeautiOptions.java (+2 -2)
-
src/dr/app/beauti/util:
BEAUTiImporter.java (+2 -1)
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rambaut
2012-08-08 10:19
#7
Rev.: 5107
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206 lines of code changed in 35 files:
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src/dr/app/beagle/evomodel/substmodel:
ComplexSubstitutionModel.java (+8),
SVSGeneralSubstitutionModel.java (+8)
-
src/dr/app/beast:
BeastDialog.java (+35 -10),
BeastMain.java (+17 -3)
-
src/dr/app/beauti/components/discrete:
DiscreteTraitsComponentOptions.java (+3 -1)
-
src/dr/app/beauti/siteModelsPanel:
SiteModelsPanel.java (new)
-
src/dr/app/pathogen:
TemporalRooting.java (-2)
-
src/dr/app/tracer/application:
TracerApp.java (+1 -1)
-
src/dr/evolution/util:
Taxon.java (-2)
-
src/dr/evomodel/coalescent:
GMRFDensityComponent.java (+4)
-
src/dr/evomodel/epidemiology:
SIRModel.java (+4)
-
src/dr/evomodel/substmodel:
ComplexSubstitutionModel.java (new),
MultivariateOUModel.java (new),
SVSGeneralSubstitutionModel.java (new)
-
src/dr/inference/distribution:
DistributionLikelihood.java (new)
-
src/dr/inference/model:
AbstractModelLikelihood.java (+4),
BooleanLikelihood.java (new),
CompoundLikelihood.java (+56 -32),
Likelihood.java (new),
PathLikelihood.java (+4),
ThreadedCompoundLikelihood.java (+4)
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src/dr/math/distributions:
MultivariatePolyaDistributionLikelihood.java (+4)
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rambaut
2012-08-04 09:47
#6
Rev.: 5100
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12 lines of code changed in 3 files:
-
src/dr/app/beast:
BeastMain.java (+2 -1)
-
src/dr/inference/model:
CompoundLikelihood.java (+4 -2)
-
src/dr/inferencexml/model:
CompoundLikelihoodParser.java (+6 -6)
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rambaut
2012-08-04 09:30
#5
Rev.: 5098
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5 lines of code changed in 1 file:
-
src/dr/inferencexml/model:
CompoundLikelihoodParser.java (+5 -5)
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rambaut
2012-08-04 03:49
#4
Rev.: 5097
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448 lines of code changed in 52 files:
-
src/dr/app/beagle/evomodel/parsers:
AncestralStateTreeLikelihoodParser.java (+25),
GammaSiteModelParser.java (+25)
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src/dr/app/beagle/evomodel/substmodel:
FrequencyModel.java (+1 -1),
MarkovJumpsSubstitutionModel.java (+25)
-
src/dr/app/beagle/evomodel/treelikelihood:
BeagleTreeLikelihood.java (+12 -3)
-
src/dr/app/beagle/tools/parsers:
BeagleSequenceSimulatorParser.java (-1)
-
src/dr/app/beauti:
BeautiFrame.java (+26 -16)
-
src/dr/app/beauti/components/ancestralstates:
AncestralStatesComponentGenerator.java (+125 -50)
-
src/dr/app/beauti/components/continuous:
ContinuousComponentGenerator.java (+14 -4)
-
src/dr/app/beauti/components/discrete:
DiscreteTraitsComponentGenerator.java (+49 -33)
-
src/dr/app/beauti/datapanel:
DataPanel.java (+10 -2)
-
src/dr/app/beauti/generator:
BaseComponentGenerator.java (new),
ComponentGenerator.java (+2 -1),
Generator.java (new),
LogGenerator.java (+31 -1),
PatternListGenerator.java (-2),
TreeLikelihoodGenerator.java (+21 -16)
-
src/dr/app/beauti/options:
BeautiOptions.java (+5),
PartitionData.java (+5),
PartitionOptions.java (+4 -4),
PartitionTreePrior.java (+4 -4)
-
src/dr/app/beauti/siteModelsPanel:
SiteModelsPanel.java (-1)
-
src/dr/app/beauti/traitspanel:
TraitsPanel.java (+8 -2)
-
src/dr/app/gui/chart:
Axis.java (new)
-
src/dr/app/tracer/analysis:
GMRFSkyrideDialog.java (+11 -3)
-
src/dr/evolution/alignment:
SimpleAlignment.java (new)
-
src/dr/evolution/tree:
Tree.java (+8 -1)
-
src/dr/evomodelxml/operators:
PopsIOTreeNodeSlideParser.java (-1)
-
src/dr/evomodelxml/speciation:
PopsIOMSCoalescentParser.java (-1),
PopsIOSpeciesBindingsParser.java (-1),
PopsIOSpeciesBindingsSpInfoParser.java (new),
PopsIOSpeciesTreeModelParser.java (-1),
PopsIOSpeciesTreePriorParser.java (new)
-
src/dr/evomodelxml/tree:
AncestralTraitParser.java (new),
TreeLoggerParser.java (+15)
-
src/dr/inference/model:
Likelihood.java (+2 -3)
-
src/dr/inferencexml/model:
CompoundLikelihoodParser.java (+3 -8)
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rambaut
2012-08-02 00:14
#3
Rev.: 5081
-
5 lines of code changed in 1 file:
-
src/dr/app/beauti/ancestralStatesPanel:
AncestralStatesOptionsPanel.java (+5 -3)
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rambaut
2012-08-01 21:44
#2
Rev.: 5080
-
478 lines of code changed in 1 file:
-
examples/release/testXML:
testTipDatePrecision.xml (new 478)
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rambaut
2012-08-01 04:12
#1
Rev.: 5079
-
7 lines of code changed in 3 files:
-
src/dr/evolution/coalescent:
CoalescentSimulator.java (+2 -2)
-
src/dr/evolution/util:
Taxon.java (+4)
-
src/dr/evomodel/coalescent:
CoalescentSimulator.java (+1 -24)