-
rambaut
2009-05-31 07:32
#101
Rev.: 1756
-
2 lines of code changed in 1 file:
-
src/dr/evomodel/beagle/treelikelihood:
BeagleTreeLikelihood.java (+2 -2)
-
rambaut
2009-05-31 04:48
#100
Rev.: 1755
-
3 lines of code changed in 1 file:
-
src/dr/evomodel/beagle/treelikelihood:
BeagleTreeLikelihood.java (+3)
-
dong.w.xie
2009-05-29 15:03
#99
Rev.: 1754
-
164 lines of code changed in 7 files:
-
src/dr/app/beauti:
BeautiFrame.java (+26 -9)
-
src/dr/app/beauti/datapanel:
DataPanel.java (+3)
-
src/dr/app/beauti/options:
TreePrior.java (+2 -2)
-
src/dr/app/beauti/traitspanel:
TraitsPanel.java (+4 -1)
-
src/dr/app/beauti/treespanel:
OldTreesPanel.java (+3 -5),
SpeciesTreesPanel.java (+123),
TreesPanel.java (+3 -5)
-
dong.w.xie
2009-05-28 16:22
#98
Rev.: 1753
-
3 lines of code changed in 1 file:
-
src/dr/app/beauti/traitspanel:
GuessTraitDialog.java (+3 -27)
-
dong.w.xie
2009-05-28 14:12
#97
Rev.: 1752
-
69 lines of code changed in 4 files:
-
src/dr/app/beauti:
BeautiFrame.java (+3 -2)
-
src/dr/app/beauti/options:
BeautiOptions.java (+19 -14),
PartitionModel.java (+46 -4)
-
src/dr/app/beauti/traitspanel:
TraitsPanel.java (+1)
-
dong.w.xie
2009-05-28 11:14
#96
Rev.: 1751
-
5 lines of code changed in 3 files:
-
src/dr/app/beauti:
BeautiFrame.java (+1 -2)
-
src/dr/app/beauti/datapanel:
DataPanel.java (+1)
-
src/dr/app/beauti/generator:
Generator.java (+3 -5)
-
dong.w.xie
2009-05-28 09:59
#95
Rev.: 1750
-
737 lines of code changed in 9 files:
-
src/dr/app/beauti:
BeautiFrame.java (+1),
GuessDatesDialog.java (del),
GuessDatesException.java (del),
TipDatesPanel.java (del)
-
src/dr/app/beauti/options:
DateGuesser.java (+1 -1)
-
src/dr/app/beauti/tipdatepanel:
GuessDatesDialog.java (+199),
GuessDatesException.java (new 11),
TipDatesPanel.java (+524)
-
src/dr/app/pathogen:
SamplesPanel.java (+1 -1)
-
rambaut
2009-05-27 23:13
#94
Rev.: 1749
-
32 lines of code changed in 3 files:
-
src/dr/evolution/datatype:
DataType.java (+12),
GeneralDataType.java (+3)
-
src/dr/evomodel/treelikelihood:
AncestralStateTreeLikelihood.java (+17 -2)
-
dong.w.xie
2009-05-27 14:29
#93
Rev.: 1748
-
12 lines of code changed in 2 files:
-
src/dr/app/beauti/options:
TraitGuesser.java (+1 -1)
-
src/dr/app/beauti/traitspanel:
TraitsPanel.java (+11 -19)
-
dong.w.xie
2009-05-27 12:58
#92
Rev.: 1747
-
144 lines of code changed in 4 files:
-
src/dr/app/beauti/options:
BeautiOptions.java (-1),
TraitGuesser.java (+66 -137)
-
src/dr/app/beauti/traitspanel:
GuessTraitDialog.java (+32 -30),
TraitsPanel.java (+46 -37)
-
dong.w.xie
2009-05-26 11:34
#91
Rev.: 1746
-
22 lines of code changed in 7 files:
-
src/dr/app/beauti:
BeautiFrame.java (+3 -2)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+1 -1)
-
src/dr/app/beauti/options:
BeautiOptions.java (+3 -9),
TraitGuesser.java (+7 -1)
-
src/dr/app/beauti/traitspanel:
CreateTraitDialog.java (+4 -3),
GuessTraitDialog.java (+1 -1),
TraitsPanel.java (+3 -3)
-
dong.w.xie
2009-05-26 11:17
#90
Rev.: 1745
-
541 lines of code changed in 10 files:
-
src/dr/app/beauti:
BeautiFrame.java (+23 -19)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+7 -7),
MultiSpeciesCoalescentGenerator.java (+7 -6),
OperatorsGenerator.java (+2 -1)
-
src/dr/app/beauti/options:
BeautiOptions.java (+23 -22),
TraitGuesser.java (+219)
-
src/dr/app/beauti/traitspanel:
CreateTraitDialog.java (+1 -1),
GuessTraitDialog.java (+190),
GuessTraitException.java (new 11),
TraitsPanel.java (+58 -40)
-
msuchard
2009-05-26 07:29
#89
Rev.: 1744
-
21 lines of code changed in 4 files:
-
src/dr/evolution/alignment:
SitePatterns.java (+10 -2)
-
src/dr/evomodel/operators:
TraitGibbsOperator.java (+6 -2)
-
src/dr/evoxml:
SitePatternsParser.java (+4 -1)
-
src/dr/geo:
KernelDensityEstimator2D.java (+1 -1)
-
rambaut
2009-05-26 02:21
#88
Rev.: 1743
-
231 lines of code changed in 2 files:
-
src/dr/evomodel/tree:
UniformRootPrior.java (+211 -149)
-
src/dr/math:
Polynomial.java (+20 -20)
-
dong.w.xie
2009-05-25 10:28
#87
Rev.: 1742
-
17 lines of code changed in 7 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+4 -2),
MultiSpeciesCoalescentGenerator.java (+2 -2),
TreePriorGenerator.java (+4 -3)
-
src/dr/app/beauti/options:
BeautiOptions.java (+2 -2),
TreePrior.java (+1 -1)
-
src/dr/app/beauti/treespanel:
OldTreesPanel.java (+2 -2),
TreesPanel.java (+2 -2)
-
jheled
2009-05-24 19:21
#86
Rev.: 1741
-
28 lines of code changed in 2 files:
-
src/dr/evolution/io:
NewickImporter.java (+16 -8)
-
src/dr/evoxml:
NewickParser.java (+12 -8)
-
dong.w.xie
2009-05-22 15:53
#85
Rev.: 1740
-
1 lines of code changed in 1 file:
-
build_BEAST_MCMC.xml (+1)
-
Sibon.Li@gmail.com
2009-05-22 12:02
#84
Rev.: 1739
-
218 lines of code changed in 3 files:
-
src/dr/inference/distribution:
InverseGaussianDistributionModel.java (+5 -5)
-
src/dr/math/distributions:
InverseGaussianDistribution.java (+77 -2)
-
src/test/dr/distibutions:
InverseGaussianDistributionTest.java (+136)
-
dong.w.xie
2009-05-22 11:20
#83
Rev.: 1738
-
36 lines of code changed in 3 files:
-
src/dr/app/beauti:
BeautiFrame.java (+14)
-
src/dr/app/beauti/generator:
MultiSpeciesCoalescentGenerator.java (+2 -11)
-
src/dr/app/beauti/options:
BeautiOptions.java (+20 -1)
-
msuchard
2009-05-22 11:14
#82
Rev.: 1737
-
4 lines of code changed in 1 file:
-
src/dr/app/tools:
TreeAnnotator.java (+4 -3)
-
nawi214
2009-05-22 09:41
#81
Rev.: 1736
-
6 lines of code changed in 1 file:
-
build_release.xml (+6 -1)
-
rambaut
2009-05-22 02:20
#80
Rev.: 1735
-
9 lines of code changed in 3 files:
-
src/dr/app/beast:
BeastMain.java (+3 -3)
-
src/dr/evomodel/treelikelihood:
TreeLikelihood.java (+4)
-
src/dr/inference/model:
LikelihoodBenchmarker.java (+2 -1)
-
dong.w.xie
2009-05-21 10:54
#79
Rev.: 1734
-
11 lines of code changed in 1 file:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+11 -3)
-
dong.w.xie
2009-05-20 14:24
#78
Rev.: 1733
-
37 lines of code changed in 1 file:
-
src/dr/app/beauti:
MCMCPanel.java (new 37)
-
dong.w.xie
2009-05-20 14:01
#77
Rev.: 1732
-
162 lines of code changed in 10 files:
-
src/dr/app/beauti:
BeautiFrame.java (+8),
MCMCPanel.java (+1 -1)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+10 -10),
InitialTreeGenerator.java (+2),
MultiSpeciesCoalescentGenerator.java (+54 -44),
TreePriorGenerator.java (+42 -21)
-
src/dr/app/beauti/options:
BeautiOptions.java (+24 -17),
TreePrior.java (+3 -1)
-
src/dr/app/beauti/treespanel:
OldTreesPanel.java (+14 -3),
TreesPanel.java (+4 -1)
-
rambaut
2009-05-20 10:42
#76
Rev.: 1731
-
9 lines of code changed in 2 files:
-
build_release.xml (+4 -5)
-
src/dr/app/tools:
TreeAnnotator.java (+5 -2)
-
Sibon.Li@gmail.com
2009-05-19 16:45
#75
Rev.: 1730
-
3 lines of code changed in 3 files:
-
src/dr/app/beast:
BeastParser.java (+1)
-
src/dr/inference/distribution:
InverseGaussianDistributionModel.java (+1 -1)
-
src/dr/math/distributions:
InverseGaussianDistribution.java (+1 -1)
-
msuchard
2009-05-19 15:27
#74
Rev.: 1729
-
18 lines of code changed in 1 file:
-
src/dr/app/tools:
TreeAnnotator.java (+18 -7)
-
msuchard
2009-05-19 12:18
#73
Rev.: 1728
-
59 lines of code changed in 3 files:
-
src/dr/evomodel/operators:
TraitGibbsOperator.java (+54 -14)
-
src/dr/geo:
GeoSpatialCollectionModel.java (+2),
GeoSpatialDistribution.java (+3 -3)
-
dong.w.xie
2009-05-19 10:50
#72
Rev.: 1727
-
89 lines of code changed in 4 files:
-
src/dr/app/beauti:
BeautiFrame.java (+1),
MCMCPanel.java (+76 -37)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+10 -10)
-
src/dr/app/beauti/options:
BeautiOptions.java (+2 -1)
-
msuchard
2009-05-19 07:07
#71
Rev.: 1726
-
3 lines of code changed in 1 file:
-
src/dr/geo:
GeoSpatialDistribution.java (+3 -1)
-
msuchard
2009-05-19 06:40
#70
Rev.: 1725
-
7 lines of code changed in 1 file:
-
src/dr/app/tools:
TreeAnnotator.java (+7 -2)
-
msuchard
2009-05-18 13:52
#69
Rev.: 1724
-
105 lines of code changed in 2 files:
-
src/dr/app/tools:
TreeAnnotator.java (+76 -58)
-
src/dr/geo:
KernelDensityEstimator2D.java (+29)
-
dong.w.xie
2009-05-18 11:34
#68
Rev.: 1723
-
113 lines of code changed in 8 files:
-
src/dr/app/beauti/components:
SequenceErrorModelComponentGenerator.java (+3 -4),
TipDateSamplingComponentGenerator.java (+2 -2)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+3 -3),
BranchRatesModelGenerator.java (+41 -44),
Generator.java (+1 -1),
InitialTreeGenerator.java (+3 -3),
PartitionModelGenerator.java (+29 -54),
TreePriorGenerator.java (+31 -39)
-
dong.w.xie
2009-05-18 11:10
#67
Rev.: 1722
-
5 lines of code changed in 1 file:
-
src/dr/app/beauti/generator:
MultiSpeciesCoalescentGenerator.java (+5 -2)
-
rambaut
2009-05-16 23:21
#66
Rev.: 1721
-
91 lines of code changed in 2 files:
-
src/dr/app/beast:
development_parsers.properties (+5 -2)
-
src/dr/inference/model:
LikelihoodBenchmarker.java (+86)
-
rambaut
2009-05-16 22:04
#65
Rev.: 1720
-
4 lines of code changed in 1 file:
-
src/dr/inference/markovchain:
MarkovChain.java (+4 -2)
-
jheled
2009-05-16 13:05
#64
Rev.: 1719
-
33 lines of code changed in 5 files:
-
src/dr/inference/markovchain:
MarkovChain.java (+6 -4)
-
src/dr/inference/mcmc:
MCMC.java (+5 -1),
MCMCOptions.java (+8),
MarginalLikelihoodEstimator.java (+13 -13)
-
src/dr/inference/ml:
MLOptimizer.java (+1 -1)
-
jheled
2009-05-16 13:03
#63
Rev.: 1718
-
140 lines of code changed in 17 files:
-
src/dr/app/beauti/generator:
OperatorsGenerator.java (+1 -2)
-
src/dr/app/beauti/options:
OperatorType.java (+1 -1)
-
src/dr/evolution/coalescent:
TreeIntervals.java (+7 -8)
-
src/dr/evomodel/tree:
RateCovarianceStatistic.java (+1 -2)
-
src/dr/evoxml:
SimpleNodeParser.java (+2 -2),
TaxonParser.java (+4 -4)
-
src/dr/inference/model:
DifferenceStatistic.java (+2 -2),
ParameterParser.java (+93 -87),
ProductStatistic.java (+3 -3),
RatioStatistic.java (+1 -3),
SumStatistic.java (+3 -3)
-
src/dr/inference/operators:
MultivariateNormalOperator.java (+3 -3),
RandomWalkOperator.java (+2 -2),
TeamOperator.java (+1 -1),
UpDownOperator.java (+7 -19)
-
src/dr/xml:
AttributeParser.java (+9 -10)
-
msuchard
2009-05-16 08:49
#62
Rev.: 1717
-
250 lines of code changed in 3 files:
-
src/dr/app/beast:
development_parsers.properties (+1)
-
src/dr/inference/operators:
RegressionGibbsEffectOperator.java (+84 -56),
RegressionMetropolizedIndicatorOperator.java (+165)
-
msuchard
2009-05-16 06:35
#61
Rev.: 1716
-
2 lines of code changed in 1 file:
-
src/dr/inference/markovchain:
MarkovChain.java (+2)
-
dong.w.xie
2009-05-15 15:48
#60
Rev.: 1715
-
79 lines of code changed in 3 files:
-
src/dr/app/beauti:
MCMCPanel.java (+23 -2)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+51 -14)
-
src/dr/app/beauti/options:
BeautiOptions.java (+5 -2)
-
alexei.drummond
2009-05-14 15:51
#59
Rev.: 1714
-
8 lines of code changed in 1 file:
-
examples/treePriors:
testCoalescent.xml (+8 -6)
-
dong.w.xie
2009-05-14 11:06
#58
Rev.: 1713
-
269 lines of code changed in 2 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+269 -223),
Generator.java (-1)
-
msuchard
2009-05-14 08:01
#57
Rev.: 1712
-
22 lines of code changed in 2 files:
-
src/dr/evomodel/substmodel:
ComplexSubstitutionModel.java (+6)
-
src/dr/evomodel/treelikelihood:
AncestralStateTreeLikelihood.java (+16 -16)
-
msuchard
2009-05-13 17:13
#56
Rev.: 1711
-
118 lines of code changed in 2 files:
-
src/dr/evomodel/operators:
InternalTraitGibbsOperator.java (+1 -20),
TraitGibbsOperator.java (+117 -21)
-
dong.w.xie
2009-05-13 16:48
#55
Rev.: 1710
-
75 lines of code changed in 9 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+10),
Generator.java (+2 -2),
MultiSpeciesCoalescentGenerator.java (+7 -13),
OperatorsGenerator.java (+14)
-
src/dr/app/beauti/options:
BeautiOptions.java (+36 -3),
ModelOptions.java (+2 -1),
OperatorType.java (+3 -1),
PartitionModel.java (-1)
-
src/dr/evomodel/operators:
TreeNodeSlide.java (+1 -1)
-
dong.w.xie
2009-05-13 14:04
#54
Rev.: 1709
-
13 lines of code changed in 2 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+4 -4),
MultiSpeciesCoalescentGenerator.java (+9 -11)
-
dong.w.xie
2009-05-13 13:34
#53
Rev.: 1708
-
247 lines of code changed in 4 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+7 -185),
Generator.java (+7 -1),
MultiSpeciesCoalescentGenerator.java (+227)
-
src/dr/evomodelxml:
BirthDeathModelParser.java (+6 -6)
-
msuchard
2009-05-13 11:41
#52
Rev.: 1707
-
4 lines of code changed in 2 files:
-
src/dr/evomodel/tree:
UniformRootPrior.java (+2 -2)
-
src/dr/math:
Polynomial.java (+2 -2)
-
msuchard
2009-05-13 11:38
#51
Rev.: 1706
-
141 lines of code changed in 1 file:
-
src/dr/math:
Polynomial.java (+141 -141)
-
msuchard
2009-05-13 11:25
#50
Rev.: 1705
-
831 lines of code changed in 4 files:
-
src/dr/evomodel/tree:
UniformRootPrior.java (+168 -244)
-
src/dr/inference/distribution:
LinearRegression.java (+2 -18)
-
src/dr/math:
LogTricks.java (+6 -4),
Polynomial.java (+655)
-
dong.w.xie
2009-05-12 16:44
#49
Rev.: 1704
-
109 lines of code changed in 7 files:
-
src/dr/app/beauti:
BeautiFrame.java (+2 -1)
-
src/dr/app/beauti/components:
SequenceErrorModelComponentOptions.java (+1 -1),
TipDateSamplingComponentOptions.java (+1 -1)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+2 -3)
-
src/dr/app/beauti/options:
BeautiOptions.java (+58 -28),
ModelOptions.java (+5 -2),
PartitionModel.java (+40 -39)
-
Sibon.Li@gmail.com
2009-05-12 15:54
#48
Rev.: 1703
-
268 lines of code changed in 2 files:
-
src/dr/inference/distribution:
InverseGaussianDistributionModel.java (+268),
ReciprocalRateDistributionModel.java (del)
-
dong.w.xie
2009-05-12 15:12
#47
Rev.: 1702
-
161 lines of code changed in 7 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+144 -15),
Generator.java (+2),
OperatorsGenerator.java (+2 -1),
TreePriorGenerator.java (+3 -3)
-
src/dr/evomodel/speciation:
SpeciesTreeBMPrior.java (+4 -4)
-
src/dr/evomodelxml:
BirthDeathModelParser.java (+4 -3)
-
src/dr/xml:
XMLParser.java (+2 -2)
-
jheled
2009-05-12 11:33
#46
Rev.: 1701
-
2 lines of code changed in 1 file:
-
src/dr/evomodel/speciation:
BirthDeathGernhard08Model.java (+2 -1)
-
dong.w.xie
2009-05-12 10:33
#45
Rev.: 1700
-
30 lines of code changed in 3 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+24 -15)
-
src/dr/evomodel/speciation:
SpeciesTreeModel.java (+5 -5)
-
src/dr/evomodel/tree:
TreeModel.java (+1 -3)
-
jheled
2009-05-12 10:17
#44
Rev.: 1699
-
315 lines of code changed in 2 files:
-
src/dr/evomodel/speciation:
SpeciesTreeBMPrior.java (+187),
SpeciesTreeSimplePrior.java (+128)
-
dong.w.xie
2009-05-11 17:04
#43
Rev.: 1698
-
738 lines of code changed in 8 files:
-
src/dr/app/beauti:
BeautiFrame.java (+4 -1)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+248 -108),
OperatorsGenerator.java (+12 -6)
-
src/dr/app/beauti/options:
BeautiOptions.java (+33 -10),
ModelOptions.java (+1 -2),
Operator.java (+5 -1),
PartitionModel.java (+433)
-
src/dr/evomodel/tree:
TreeModel.java (+2)
-
rambaut
2009-05-11 11:25
#42
Rev.: 1697
-
5 lines of code changed in 1 file:
-
src/dr/evomodel/tree:
UniformRootPrior.java (+5 -1)
-
msuchard
2009-05-10 10:22
#41
Rev.: 1696
-
201 lines of code changed in 1 file:
-
src/dr/evomodel/tree:
UniformRootPrior.java (+201 -4)
-
jheled
2009-05-09 10:57
#40
Rev.: 1695
-
1 lines of code changed in 1 file:
-
src/dr/evomodel/operators:
ExchangeOperator.java (+1 -1)
-
jheled
2009-05-09 10:52
#39
Rev.: 1694
-
74 lines of code changed in 6 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+32 -37),
Generator.java (+7 -7),
OperatorsGenerator.java (+19 -23)
-
src/dr/app/beauti/options:
OperatorType.java (+3 -1)
-
src/dr/app/oldbeauti:
BeastGenerator.java (+7 -7)
-
src/dr/evomodel/operators:
NodeHeightScaleOperator.java (+6 -6)
-
msuchard
2009-05-09 04:49
#38
Rev.: 1693
-
595 lines of code changed in 11 files:
-
examples:
testMixedModel.xml (new 148)
-
src/dr/app/beast:
development_parsers.properties (+2 -1),
release_parsers.properties (+1 -1)
-
src/dr/inference/distribution:
GeneralizedLinearModel.java (+50 -19),
LinearRegression.java (+31 -3)
-
src/dr/inference/operators:
BitFlipOperator.java (+25 -16),
NormalGammaPrecisionGibbsOperator.java (+1 -1),
RegressionGibbsEffectOperator.java (+195),
RegressionGibbsOperator.java (del),
RegressionGibbsPrecisionOperator.java (new 141)
-
src/test/dr/evomodel/speciation:
RLYModelTest.java (+1 -1)
-
dong.w.xie
2009-05-08 16:50
#37
Rev.: 1692
-
48 lines of code changed in 4 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+9 -2),
InitialTreeGenerator.java (+4 -3),
OperatorsGenerator.java (-1),
TreePriorGenerator.java (+35 -36)
-
dong.w.xie
2009-05-08 15:24
#36
Rev.: 1691
-
885 lines of code changed in 9 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+414 -411),
BranchRatesModelGenerator.java (+2 -12),
Generator.java (+14 -4),
InitialTreeGenerator.java (-12),
OperatorsGenerator.java (+451),
TreeLikelihoodGenerator.java (-10),
TreeModelGenerator.java (+1 -15),
TreePriorGenerator.java (-11)
-
src/dr/app/beauti/options:
BeautiOptions.java (+3 -2)
-
dong.w.xie
2009-05-07 11:43
#35
Rev.: 1690
-
152 lines of code changed in 6 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+21 -9),
BranchRatesModelGenerator.java (+63 -53),
InitialTreeGenerator.java (+11 -11),
TreeLikelihoodGenerator.java (+3 -3),
TreeModelGenerator.java (+12 -11),
TreePriorGenerator.java (+42 -41)
-
jheled
2009-05-07 08:01
#34
Rev.: 1689
-
335 lines of code changed in 1 file:
-
src/dr/evomodel/operators:
INS.java (+335)
-
jheled
2009-05-07 07:47
#33
Rev.: 1688
-
231 lines of code changed in 12 files:
-
src/dr/app/beast:
BeastParser.java (+3 -3)
-
src/dr/app/beauti:
BeastImporter.java (new 12),
XMLWriter.java (new 55)
-
src/dr/app/beauti/components:
TipDateSamplingComponentGenerator.java (+3 -6)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+87 -107),
BranchRatesModelGenerator.java (+15 -15),
InitialTreeGenerator.java (+2 -2)
-
src/dr/app/beauti/options:
BeautiOptions.java (+9 -6)
-
src/dr/app/coalgen:
CoalGenData.java (+3 -2)
-
src/dr/app/oldbeauti:
BeastGenerator.java (+18 -18),
BeautiOptions.java (+11 -8)
-
src/dr/evomodel/treelikelihood:
SequenceErrorModel.java (+13 -11)
-
jheled
2009-05-07 07:45
#32
Rev.: 1687
-
2 lines of code changed in 3 files:
-
src/dr/evomodel/MSSD:
ALSTreeLikelihood.java (+1 -1)
-
src/dr/evoxml:
TaxaParser.java (+1 -1)
-
rambaut
2009-05-07 00:33
#31
Rev.: 1686
-
44 lines of code changed in 3 files:
-
src/dr/app/beauti:
BeautiFrame.java (-7)
-
src/dr/app/beauti/components:
SequenceErrorModelComponentGenerator.java (+14 -10),
SequenceErrorModelComponentOptions.java (+30 -25)
-
jheled
2009-05-06 22:58
#30
Rev.: 1685
-
33 lines of code changed in 2 files:
-
src/dr/app/beauti/components:
SequenceErrorModelComponentGenerator.java (+6 -13),
SequenceErrorModelComponentOptions.java (+27 -19)
-
rambaut
2009-05-06 21:35
#29
Rev.: 1684
-
411 lines of code changed in 18 files:
-
src/dr/app/beauti:
BeautiFrame.java (+12 -14),
TipDatesPanel.java (new 2)
-
src/dr/app/beauti/components:
ComponentFactory.java (new 13),
SequenceErrorModelComponentFactory.java (new 35),
TipDateSamplingComponent.java (del),
TipDateSamplingComponentFactory.java (new 35),
TipDateSamplingComponentGenerator.java (+99),
TipDateSamplingComponentOptions.java (+97)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+72 -71),
BranchRatesModelGenerator.java (+2 -1),
Generator.java (+10 -2),
InitialTreeGenerator.java (+4 -3),
PartitionModelGenerator.java (+2 -1),
TreeLikelihoodGenerator.java (+4 -4),
TreeModelGenerator.java (+6 -5),
TreePriorGenerator.java (+7 -6)
-
src/dr/app/beauti/options:
BeautiOptions.java (+10),
ModelOptions.java (+1 -1)
-
Sibon.Li@gmail.com
2009-05-06 17:41
#28
Rev.: 1683
-
1 lines of code changed in 1 file:
-
src/dr/math/distributions:
InverseGaussianDistribution.java (+1 -21)
-
Sibon.Li@gmail.com
2009-05-06 17:37
#27
Rev.: 1682
-
240 lines of code changed in 1 file:
-
src/dr/math/distributions:
InverseGaussianDistribution.java (+240)
-
dong.w.xie
2009-05-06 16:50
#26
Rev.: 1681
-
66 lines of code changed in 3 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+50 -16),
InitialTreeGenerator.java (+1 -1),
TreeLikelihoodGenerator.java (+15 -11)
-
dong.w.xie
2009-05-06 15:16
#25
Rev.: 1680
-
6 lines of code changed in 2 files:
-
src/dr/app/beauti/components:
SequenceErrorModelComponentOptions.java (+1 -1)
-
src/dr/app/beauti/modelsPanel:
ModelsPanel.java (+5 -1)
-
dong.w.xie
2009-05-06 11:10
#24
Rev.: 1679
-
0 lines of code changed in 2 files:
-
src/dr/app/beauti:
BeautiFrame.java (-12),
TipSpeciesPanel.java (del)
-
jheled
2009-05-06 10:32
#23
Rev.: 1678
-
1 lines of code changed in 1 file:
-
src/dr/xml:
XMLParser.java (+1 -1)
-
jheled
2009-05-06 10:31
#22
Rev.: 1677
-
29 lines of code changed in 2 files:
-
src/dr/app/tools:
LogCombiner.java (+1 -1),
LogCombinerDialog.java (+28 -29)
-
jheled
2009-05-06 10:31
#21
Rev.: 1676
-
684 lines of code changed in 28 files:
-
src/dr/app/beauti:
BeastImporter.java (+13 -12)
-
src/dr/app/beauti/components:
SequenceErrorModelComponentGenerator.java (+7 -8),
TipDateSamplingComponent.java (new 14)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+114 -108),
BranchRatesModelGenerator.java (+69 -67),
Generator.java (+5 -5),
InitialTreeGenerator.java (+12 -11),
PartitionModelGenerator.java (+43 -40),
TreeLikelihoodGenerator.java (+22 -19),
TreeModelGenerator.java (+16 -15),
TreePriorGenerator.java (+69 -70)
-
src/dr/app/beauti/options:
BeautiOptions.java (+8 -5)
-
src/dr/app/oldbeauti:
BeastGenerator.java (+259 -257),
BeautiOptions.java (+10 -8)
-
src/dr/evomodel/arg:
ARGModel.java (+1 -1),
ARGRatePrior.java (+1 -1)
-
src/dr/evomodel/beagle/parsers:
TreeLikelihoodParser.java (+3 -2)
-
src/dr/evomodel/branchratemodel:
BranchRateModel.java (+1 -2),
StrictClockBranchRates.java (+1 -1)
-
src/dr/evomodel/clock:
UCLikelihood.java (+2 -2)
-
src/dr/evoxml:
AlignmentParser.java (+1 -1),
AscertainedSitePatternsParser.java (+1 -1),
AttributePatternsParser.java (+1 -1),
PatternSubSetParser.java (new),
SitePatternsParser.java (+1 -1)
-
src/dr/geo:
Polygon2D.java (+8 -9)
-
src/dr/util:
Identifiable.java (+1 -1)
-
jheled
2009-05-06 09:58
#20
Rev.: 1675
-
3 lines of code changed in 1 file:
-
src/dr/app/beast:
BeastParser.java (+3 -3)
-
jheled
2009-05-06 09:55
#19
Rev.: 1674
-
155 lines of code changed in 16 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+3 -3),
BranchRatesModelGenerator.java (+10 -10),
PartitionModelGenerator.java (+4 -3),
TreeLikelihoodGenerator.java (+7 -4),
TreeModelGenerator.java (+12 -10)
-
src/dr/app/beauti/options:
BeautiOptions.java (+24 -24),
ClockType.java (+3)
-
src/dr/app/oldbeauti:
BeastGenerator.java (+32 -30),
BeautiOptions.java (+42 -40)
-
src/dr/app/seqgen:
SequenceSimulator.java (+5 -12)
-
src/dr/evomodel/arg:
ARGModel.java (+2 -2)
-
src/dr/evomodel/beagle/parsers:
GTRParser.java (+3 -5),
GammaSiteModelParser.java (+4 -3)
-
src/dr/evomodel/sitemodel:
GammaSiteModel.java (+1 -2),
SiteModel.java (+2)
-
src/dr/evomodel/substmodel:
BinaryCovarionModel.java (+1 -1)
-
msuchard
2009-05-06 09:06
#18
Rev.: 1673
-
39 lines of code changed in 1 file:
-
src/dr/evomodel/tree:
UniformRootPrior.java (+39 -25)
-
jheled
2009-05-06 09:06
#17
Rev.: 1672
-
114 lines of code changed in 22 files:
-
src/dr/app/beast:
BeastParser.java (+3 -3)
-
src/dr/app/beauti:
BeautiFrame.java (+2 -5)
-
src/dr/app/beauti/generator:
BranchRatesModelGenerator.java (+18 -13),
InitialTreeGenerator.java (+11 -8),
TreeModelGenerator.java (+32 -15)
-
src/dr/app/beauti/options:
ClockType.java (+2)
-
src/dr/app/oldbeauti:
BeastGenerator.java (+12 -12)
-
src/dr/evolution/coalescent:
Coalescent.java (+1 -1)
-
src/dr/evomodel/arg:
ARGModel.java (+4 -3)
-
src/dr/evomodel/arg/operators:
ARGAddRemoveEventOperator.java (+3 -6),
ARGReassortmentOperator.java (+2 -1),
ObsoleteARGAddRemoveEventOperator.java (+2 -1),
ObsoleteARGNewEventOperator.java (+2 -1)
-
src/dr/evomodel/clock:
ACLikelihood.java (+1 -1),
RateEvolutionLikelihood.java (+2),
UCLikelihood.java (+1 -1)
-
src/dr/evomodel/coalescent:
CoalescentSimulator.java (+3 -2),
OldAbstractCoalescentLikelihood.java (+1 -1)
-
src/dr/evoxml:
UPGMATreeParser.java (+3 -2)
-
src/dr/xml:
AbstractXMLObjectParser.java (+5 -6)
-
src/test/dr/evomodel/arg/operators:
ARGAddRemoveOperatorTest.java (+2 -2)
-
src/test/dr/evomodel/speciation:
YuleModelTest.java (+2 -1)
-
msuchard
2009-05-06 06:56
#16
Rev.: 1671
-
53 lines of code changed in 1 file:
-
src/dr/evomodel/tree:
UniformRootPrior.java (+53 -11)
-
rambaut
2009-05-06 03:05
#15
Rev.: 1670
-
216 lines of code changed in 17 files:
-
src/dr/app/beauti:
BeautiFrame.java (+22 -18),
BeautiTester.java (+1 -1),
CommandLineBeauti.java (+1 -1)
-
src/dr/app/beauti/components:
SequenceErrorModelComponent.java (del),
SequenceErrorModelComponentGenerator.java (+94),
SequenceErrorModelComponentOptions.java (+50)
-
src/dr/app/beauti/generator:
BaseComponentGenerator.java (+1 -1),
BeastGenerator.java (+20 -18),
BranchRatesModelGenerator.java (+2 -2),
Generator.java (+7 -6),
InitialTreeGenerator.java (+2 -2),
PartitionModelGenerator.java (+2 -2),
TreeLikelihoodGenerator.java (+2 -2),
TreeModelGenerator.java (+2 -2),
TreePriorGenerator.java (+2 -2)
-
src/dr/app/beauti/modelsPanel:
ModelsPanel.java (+4 -3)
-
src/dr/app/beauti/treespanel:
TreeDisplayPanel.java (+4 -2)
-
dong.w.xie
2009-05-05 17:34
#14
Rev.: 1669
-
95 lines of code changed in 4 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+11 -5),
InitialTreeGenerator.java (+16 -5),
TreeModelGenerator.java (+28 -31),
TreePriorGenerator.java (+40 -50)
-
dong.w.xie
2009-05-05 14:53
#13
Rev.: 1668
-
41 lines of code changed in 2 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+28 -7),
TreeLikelihoodGenerator.java (+13 -6)
-
dong.w.xie
2009-05-05 14:50
#12
Rev.: 1667
-
10 lines of code changed in 2 files:
-
src/dr/app/beauti:
BeautiFrame.java (+5)
-
src/dr/app/beauti/datapanel:
DataPanel.java (+5 -1)
-
dong.w.xie
2009-05-04 16:45
#11
Rev.: 1666
-
92 lines of code changed in 3 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+32 -16),
TreeModelGenerator.java (+29 -13),
TreePriorGenerator.java (+31 -8)
-
msuchard
2009-05-02 05:02
#10
Rev.: 1665
-
5 lines of code changed in 1 file:
-
src/dr/evomodel/continuous:
CartogramDiffusionModel.java (+5 -5)
-
msuchard
2009-05-02 04:02
#9
Rev.: 1664
-
230 lines of code changed in 4 files:
-
src/dr/evomodel/continuous:
CartogramDiffusionModel.java (+9 -8),
MixtureCartogramDiffusionModel.java (+1 -1)
-
src/dr/geo:
NewPolygon2D.java (+217),
Polygon2D.java (+3)
-
dong.w.xie
2009-05-01 14:55
#8
Rev.: 1663
-
51 lines of code changed in 2 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+50 -12)
-
src/dr/app/beauti/options:
BeautiOptions.java (+1)
-
msuchard
2009-05-01 13:14
#7
Rev.: 1662
-
190 lines of code changed in 4 files:
-
src/dr/app/beast:
development_parsers.properties (+1)
-
src/dr/evomodel/continuous:
CartogramDiffusionModel.java (+69 -43),
MixtureCartogramDiffusionModel.java (+115)
-
src/dr/geo/cartogram:
CartogramMapping.java (+5)
-
jheled
2009-05-01 09:56
#6
Rev.: 1661
-
66 lines of code changed in 6 files:
-
src/dr/evomodel/coalescent:
CoalescentLikelihood.java (-3)
-
src/dr/evomodel/substmodel:
FrequencyModel.java (+1 -1),
GTR.java (+1 -1),
GeneralSubstitutionModel.java (+1 -2)
-
src/dr/inference/model:
DummyModel.java (new 60)
-
src/dr/xml:
XMLParser.java (+3 -3)
-
jheled
2009-05-01 09:55
#5
Rev.: 1660
-
5 lines of code changed in 2 files:
-
src/dr/math:
Binomial.java (new)
-
jheled
2009-05-01 09:27
#4
Rev.: 1659
-
42 lines of code changed in 2 files:
-
src/dr/app/beauti:
BeautiFrame.java (+37 -38)
-
src/dr/app/util:
Utils.java (+5 -1)
-
msuchard
2009-05-01 08:54
#3
Rev.: 1658
-
292 lines of code changed in 5 files:
-
src/dr/app/beast:
development_parsers.properties (+1 -1)
-
src/dr/geo:
GeoSpatialCollectionModel.java (+5 -4),
GeoSpatialDistribution.java (+43 -12),
SpatialTemporalPolygon.java (del)
-
src/dr/inference/model:
SplineBasis.java (+243)
-
bloomquist
2009-05-01 07:30
#2
Rev.: 1657
-
18 lines of code changed in 3 files:
-
examples:
arg-ecoli.xml (new 6),
arg-lepto.xml (new 6),
arg-rokas.xml (new 6)
-
bloomquist
2009-05-01 07:15
#1
Rev.: 1656
-
33 lines of code changed in 1 file:
-
src/dr/evomodel/arg/operators:
ARGAddRemoveEventOperator.java (+33 -14)