-
rambaut
2007-08-31 04:09
#69
Rev.: 532
-
41 lines of code changed in 2 files:
-
src/dr/evomodel/substmodel:
YangCodonModel.java (+40)
-
src/dr/inference/model:
RatioStatistic.java (+1 -2)
-
rambaut
2007-08-29 01:07
#68
Rev.: 531
-
92 lines of code changed in 2 files:
-
src/dr/app/tracer/analysis:
BayesFactorsDialog.java (+3 -3),
BayesFactorsFrame.java (+89 -24)
-
alexei.drummond
2007-08-28 21:43
#67
Rev.: 530
-
130 lines of code changed in 2 files:
-
src/test/dr/evomodel/substmodel:
BinaryCovarionModelTest.java (+6 -2),
TwoStateCovarionModelTest.java (+124 -119)
-
alexei.drummond
2007-08-27 00:53
#66
Rev.: 529
-
1388 lines of code changed in 8 files:
-
src/dr/evomodel/substmodel:
AbstractCovarionModel.java (+882),
BinaryCovarionModel.java (+212),
CovarionFrequencyModel.java (+54),
FrequencyModel.java (+5 -5)
-
src/dr/matrix:
ConcreteMatrix.java (new)
-
src/test/dr/evomodel/substmodel:
BinaryCovarionModelTest.java (+217),
TwoStateCovarionModelTest.java (+3 -1)
-
rambaut
2007-08-24 04:31
#65
Rev.: 528
-
186 lines of code changed in 7 files:
-
build_release.xml (+2),
tracer_release.xml (+102)
-
src/dr/app/beast:
BeastParser.java (+10)
-
src/dr/evolution/tree:
MutableTree.java (+1 -1)
-
src/dr/evomodel/transmission:
TransmissionHistoryModel.java (+7 -3),
TransmissionStatistic.java (+49 -17)
-
src/dr/inference/model:
Statistic.java (+15 -8)
-
rambaut
2007-08-23 22:29
#64
Rev.: 527
-
379 lines of code changed in 1 file:
-
src/dr/app/beauti:
BeastGenerator.java (+379 -379)
-
rambaut
2007-08-23 22:24
#63
Rev.: 526
-
29 lines of code changed in 2 files:
-
src/dr/app/beauti:
BeastGenerator.java (+23 -23)
-
src/dr/util:
Attribute.java (+6 -13)
-
rambaut
2007-08-23 03:37
#62
Rev.: 525
-
101 lines of code changed in 4 files:
-
src/dr/app/beauti:
BeastGenerator.java (+15 -15)
-
src/dr/evolution/coalescent:
Coalescent.java (+13 -9)
-
src/dr/inference/model:
Parameter.java (+71 -71)
-
src/dr/util:
Attribute.java (+2 -2)
-
alexei.drummond
2007-08-21 14:27
#61
Rev.: 524
-
147 lines of code changed in 2 files:
-
src/test/dr/evomodel/substmodel:
CovarionHKYTest.java (+146 -105),
TwoStateCovarionModelTest.java (+1 -1)
-
alexei.drummond
2007-08-21 12:40
#60
Rev.: 523
-
237 lines of code changed in 4 files:
-
src/dr/evomodel/substmodel:
AbstractCovarionDNAModel.java (+6 -3),
FrequencyModel.java (+19)
-
src/test/dr/evomodel/substmodel:
CovarionHKYTest.java (+210),
TwoStateCovarionModelTest.java (+2 -2)
-
msuchard
2007-08-21 08:38
#59
Rev.: 522
-
288 lines of code changed in 5 files:
-
examples:
testCTMCMap.xml (+280 -275)
-
examples/treePriors:
testGMRFCoalescent.xml (+1 -1)
-
src/dr/evomodel/coalescent:
GMRFSkylineLikelihood.java (+2 -43)
-
src/dr/evomodel/coalescent/operators:
GMRFSkylineBlockUpdateOperator.java (+5 -39),
GMRFSkylineFixedEffectsGibbsOperator.java (-4)
-
msuchard
2007-08-21 08:32
#58
Rev.: 521
-
73 lines of code changed in 1 file:
-
src/dr/app/tools:
TreeAnnotator.java (+73 -35)
-
alexei.drummond
2007-08-20 17:19
#57
Rev.: 520
-
143 lines of code changed in 2 files:
-
src/dr/evomodel/substmodel:
TwoStateCovarionModel.java (-3)
-
src/test/dr/evomodel/substmodel:
TwoStateCovarionModelTest.java (+143 -18)
-
alexei.drummond
2007-08-19 21:06
#56
Rev.: 519
-
18 lines of code changed in 2 files:
-
src/dr/evomodel/substmodel:
TwoStateCovarionModel.java (+17 -19)
-
src/test/dr/evomodel/substmodel:
TwoStateCovarionModelTest.java (+1 -1)
-
alexei.drummond
2007-08-19 21:01
#55
Rev.: 518
-
4872 lines of code changed in 46 files:
-
src/dr/app/beauti:
BeastGenerator.java (+359 -288),
BeautiOptions.java (+4 -4),
OperatorsPanel.java (+152 -145)
-
src/dr/evomodel/coalescent/operators:
BayesianSkylineGibbsOperator.java (+383 -381),
GMRFSkylineBlockUpdateOperator.java (+4 -15),
GMRFSkylineFixedEffectsGibbsOperator.java (+4 -6),
SampleNonActiveGibbsOperator.java (+14 -14)
-
src/dr/evomodel/indel:
IstvanOperator.java (+195 -186)
-
src/dr/evomodel/operators:
CategoryOperator.java (+83 -72),
ColouredExchangeOperator.java (+185 -162),
ColouredOperator.java (+81 -54),
ColouredSubtreeSlideOperator.java (+59 -35),
ECR.java (new 121),
ExchangeOperator.java (+158 -133),
FixedColouredOperator.java (+86 -61),
NNI.java (+130 -140),
RLCNarrowExchangeOperator.java (+97 -84),
RateExchangeOperator.java (+50 -40),
SPR.java (new 172),
SubtreeSlideOperator.java (+4 -4),
WilsonBalding.java (+139 -136)
-
src/dr/evomodel/substmodel:
TwoStateCovarionModel.java (+21 -10)
-
src/dr/inference/operators:
BitFlipOperator.java (+71 -64),
BitSwapOperator.java (+83 -60),
CenteredScaleOperator.java (+161 -139),
DeltaExchangeOperator.java (+177 -154),
InternalTraitGibbsOperator.java (+112 -93),
LNVarianceOperator.java (+58 -57),
MCMCOperator.java (+101 -92),
MultivariateNormalOperator.java (+161 -149),
OperatorSchedule.java (+8 -7),
OperatorUtils.java (new),
PrecisionMatrixGibbsOperator.java (+144 -126),
RandomWalkOnMapOperator.java (+160 -151),
RandomWalkOperator.java (+140 -153),
ScaleOperator.java (+176 -184),
SetOperator.java (+86 -69),
SimpleMCMCOperator.java (+152 -126),
SimpleOperatorSchedule.java (+121 -110),
SwapOperator.java (+64 -53),
UniformOperator.java (+107 -84),
UpDownOperator.java (+179 -162)
-
src/dr/util:
Attribute.java (+36 -25)
-
src/test/dr/evomodel/substmodel:
TwoStateCovarionModelTest.java (+18 -7)
-
rambaut
2007-08-18 04:27
#54
Rev.: 517
-
1 lines of code changed in 1 file:
-
src/dr/app/tools:
TreeAnnotator.java (+1 -1)
-
msuchard
2007-08-17 11:20
#53
Rev.: 514
-
36 lines of code changed in 3 files:
-
src/dr/evomodel/coalescent:
GMRFSkylineLikelihood.java (+12 -3)
-
src/dr/evomodel/coalescent/operators:
GMRFSkylineBlockUpdateOperator.java (+3 -1),
GMRFSkylineFixedEffectsGibbsOperator.java (+21 -21)
-
rambaut
2007-08-17 03:18
#52
Rev.: 513
-
7 lines of code changed in 1 file:
-
src/dr/app/tracer/analysis:
BayesFactorsFrame.java (+7)
-
rambaut
2007-08-17 03:12
#51
Rev.: 512
-
279 lines of code changed in 4 files:
-
src/dr/app/tracer/analysis:
BayesFactorsDialog.java (+191 -143),
BayesFactorsFrame.java (+25 -14)
-
src/dr/inference/trace:
MarginalLikelihoodAnalysis.java (+49 -31)
-
src/dr/util:
TaskListener.java (new 14)
-
alexei.drummond
2007-08-16 20:48
#50
Rev.: 509
-
51 lines of code changed in 1 file:
-
src/test/dr/evomodel/substmodel:
TwoStateCovarionModelTest.java (+51)
-
rambaut
2007-08-16 20:10
#49
Rev.: 508
-
319 lines of code changed in 5 files:
-
src/dr/app/tracer/analysis:
BayesFactorsDialog.java (+154 -111),
BayesFactorsFrame.java (+155),
MarginalLikelihoodDialog.java (del)
-
src/dr/app/tracer/application:
TracerFrame.java (+2 -9)
-
src/dr/inference/trace:
MarginalLikelihoodAnalysis.java (+8)
-
rambaut
2007-08-16 10:52
#48
Rev.: 507
-
465 lines of code changed in 6 files:
-
src/dr/app/tracer/analysis:
BayesFactorsDialog.java (+172)
-
src/dr/app/tracer/application:
AnalysisMenuFactory.java (+3 -3),
AnalysisMenuHandler.java (+1 -1),
TracerFrame.java (+10 -10)
-
src/dr/inference/trace:
MarginalLikelihoodAnalysis.java (+271 -247),
Trace.java (+8 -2)
-
rambaut
2007-08-16 03:38
#47
Rev.: 505
-
270 lines of code changed in 4 files:
-
src/dr/app/beauti:
BeautiOptions.java (+6),
PriorDialog.java (+250 -242),
TaxaPanel.java (+1)
-
src/dr/gui/chart:
PDFPlot.java (+13 -14)
-
rambaut
2007-08-16 03:38
#46
Rev.: 504
-
23 lines of code changed in 2 files:
-
src/dr/evolution/util:
Taxa.java (+21 -22)
-
src/dr/evomodel/coalescent:
CoalescentSimulator.java (+2 -2)
-
rambaut
2007-08-16 02:41
#45
Rev.: 503
-
7 lines of code changed in 4 files:
-
src/dr/app/tracer/application:
TracerFrame.java (+4 -4)
-
src/dr/app/tracer/traces:
DensityPanel.java (+1 -1),
RawTracePanel.java (+1 -1),
TracePanel.java (+1 -1)
-
rambaut
2007-08-14 21:04
#44
Rev.: 502
-
4 lines of code changed in 3 files:
-
build_release.xml (+3 -1)
-
src/dr/app/tracer/application:
TracerApp.java (+1 -1)
-
src/dr/inference/model:
MeanStatistic.java (-1)
-
bloomquist
2007-08-14 15:16
#43
Rev.: 501
-
41 lines of code changed in 2 files:
-
src/dr/evomodel/coalescent:
GMRFSkylineLikelihood.java (+4)
-
src/dr/evomodel/coalescent/operators:
GMRFSkylineFixedEffectsGibbsOperator.java (+37 -3)
-
msuchard
2007-08-14 12:59
#42
-
1450 lines of code changed in 11 files:
-
examples/treePriors:
testGMRFCoalescent.xml (+551 -168)
-
src/dr/app/beastdev:
BeastParser.java (+1 -1)
-
src/dr/evomodel/coalescent:
GMRFSkylineLikelihood.java (+215 -203)
-
src/dr/evomodel/coalescent/operators:
GMRFSkylineBlockUpdateOperator.java (+112 -84),
GMRFSkylineFixedEffectsGibbsOperator.java (+133),
GMRFSkylineGibbsOperator.java (del)
-
src/dr/inference/distribution:
MultivariateDistributionLikelihood.java (+105 -104),
UniformDistributionModel.java (+143 -101)
-
src/dr/math:
MultivariateDistribution.java (+6 -2),
MultivariateNormalDistribution.java (+79 -69),
WishartDistribution.java (+105 -95)
-
bloomquist
2007-08-14 09:28
#41
Rev.: 498
-
712 lines of code changed in 4 files:
-
examples/treePriors:
testGMRFCoalescent.xml (+167 -51)
-
src/dr/evomodel/coalescent:
GMRFSkylineLikelihood.java (+471 -418),
GMRFTestLikelihood.java (+16 -6)
-
src/dr/evomodel/coalescent/operators:
GMRFSkylineBlockUpdateOperator.java (+58 -47)
-
rambaut
2007-08-14 09:05
#40
Rev.: 497
-
5 lines of code changed in 2 files:
-
src/dr/inference/trace:
LogFileTraces.java (+3 -1),
Trace.java (+2 -2)
-
rambaut
2007-08-14 08:45
#39
Rev.: 496
-
2 lines of code changed in 1 file:
-
src/dr/inference/trace:
Trace.java (+2 -2)
-
alexei.drummond
2007-08-13 19:56
#38
Rev.: 495
-
77 lines of code changed in 1 file:
-
src/test/dr/evomodel/substmodel:
TwoStateCovarionModelTest.java (+77)
-
alexei.drummond
2007-08-12 23:25
#37
Rev.: 494
-
218 lines of code changed in 8 files:
-
lib:
junit-4.4.jar (new)
-
src/dr/evolution/datatype:
TwoStateCovarion.java (+1 -1)
-
src/dr/evomodel/substmodel:
AbstractCovarionDNAModel.java (-62),
AbstractSubstitutionModel.java (+8 -1),
CovarionHKY.java (+1 -1),
SubstitutionModel.java (+18 -18),
SubstitutionModelUtils.java (new 120),
TwoStateCovarionModel.java (+70 -25)
-
alexei.drummond
2007-08-12 16:52
#36
Rev.: 493
-
96 lines of code changed in 3 files:
-
examples:
testCovarionHKY.xml (+18 -6)
-
src/dr/evomodel/substmodel:
AbstractCovarionDNAModel.java (+62 -1),
CovarionHKY.java (+16 -4)
-
alexei.drummond
2007-08-11 23:48
#35
Rev.: 492
-
77 lines of code changed in 3 files:
-
examples:
testCovarionHKY.xml (+1 -1)
-
src/dr/evomodel/substmodel:
AbstractCovarionDNAModel.java (+76 -32),
CovarionHKY.java (-1)
-
alexei.drummond
2007-08-11 22:35
#34
Rev.: 491
-
739 lines of code changed in 10 files:
-
examples:
testCovarionHKY.xml (+328),
testLinearBSP.xml (del)
-
examples/treePriors:
testLinearBSP.xml (new 358)
-
src/dr/app/beast:
BeastParser.java (+3)
-
src/dr/app/beastdev:
BeastParser.java (+3 -3)
-
src/dr/evolution/datatype:
HiddenNucleotides.java (+2 -3)
-
src/dr/evomodel/substmodel:
AbstractCovarionDNAModel.java (+8 -5),
CovarionHKY.java (-4),
FrequencyModel.java (+2 -2)
-
src/dr/evoxml:
HiddenNucleotideParser.java (new 35)
-
alexei.drummond
2007-08-11 21:18
#33
Rev.: 490
-
2512 lines of code changed in 34 files:
-
examples:
constrainedTaxaTest1.xml (del),
constrainedTaxaTest2.xml (del),
constrainedTaxaTest3.xml (del),
constrainedTaxaTest4.xml (del),
constrainedTaxaTest5.xml (del),
constrainedTaxaTest6.xml (del),
constrainedTaxaTest7.xml (del),
constrainedTaxaTest8.xml (del),
constrainedTaxaTest9.xml (del),
testBSP.xml (del),
testBirthDeath.xml (del),
testBirthDeathPrior.xml (del),
testCoalescent.xml (del),
testGMRFCoalescent.xml (del),
testYule.xml (del),
testYuleModel.xml (del),
testYulePrior.xml (del)
-
examples/calibrations:
constrainedTaxaTest1.xml (new 75),
constrainedTaxaTest2.xml (new 76),
constrainedTaxaTest3.xml (+92),
constrainedTaxaTest4.xml (new 94),
constrainedTaxaTest5.xml (+111),
constrainedTaxaTest6.xml (new 78),
constrainedTaxaTest7.xml (+101),
constrainedTaxaTest8.xml (new 98),
constrainedTaxaTest9.xml (new 102)
-
examples/treePriors:
testBSP.xml (new 357),
testBirthDeath.xml (new 221),
testBirthDeathPrior.xml (new 201),
testCoalescent.xml (+172),
testGMRFCoalescent.xml (+125),
testYule.xml (+215),
testYuleModel.xml (+110),
testYulePrior.xml (+284)
-
alexei.drummond
2007-08-11 19:49
#32
Rev.: 489
-
1382 lines of code changed in 12 files:
-
src/dr/app/beast:
BeastParser.java (+2 -3)
-
src/dr/app/beastdev:
BeastParser.java (+1 -1)
-
src/dr/evolution/datatype:
HiddenNucleotides.java (+198 -158),
TwoStateCovarion.java (+79 -72)
-
src/dr/evomodel/substmodel:
AbstractCovarionDNAModel.java (+164),
AbstractSubstitutionModel.java (+182 -326),
CovarionGTR.java (+210),
CovarionHKY.java (+157),
CovarionSubstitutionModel.java (del),
GTR.java (+235 -224),
RelaxedClockHKY.java (del),
TwoStateCovarionModel.java (+154)
-
msuchard
2007-08-11 06:46
#31
Rev.: 488
-
270 lines of code changed in 1 file:
-
src/dr/evomodel/tree:
TreeLogger.java (+270 -258)
-
msuchard
2007-08-11 06:34
#30
Rev.: 487
-
207 lines of code changed in 1 file:
-
src/dr/app/beastdev:
BeastParser.java (+207 -208)
-
msuchard
2007-08-11 06:25
#29
Rev.: 486
-
1373 lines of code changed in 5 files:
-
examples:
testAncestralReconstruction.xml (new 245),
testCTMCMap.xml (+304)
-
src/dr/app/beastdev:
BeastParser.java (+208 -206)
-
src/dr/evomodel/treelikelihood:
AbstractLikelihoodCore.java (+381 -362),
AncestralStateTreeLikelihood.java (+235)
-
rambaut
2007-08-11 00:31
#28
Rev.: 485
-
2 lines of code changed in 1 file:
-
src/dr/evomodel/treelikelihood:
AdvancedTreeLikelihood.java (+2 -1)
-
alexei.drummond
2007-08-10 16:49
#27
Rev.: 483
-
126 lines of code changed in 3 files:
-
src/dr/evomodel/substmodel:
FrequencyModel.java (+41 -20)
-
src/dr/evomodel/tree:
TreeTraceAnalysisParser.java (+57 -44)
-
src/dr/inference/operators:
CoercableMCMCOperator.java (+28 -26)
-
msuchard
2007-08-10 10:52
#26
Rev.: 482
-
57 lines of code changed in 1 file:
-
src/dr/evomodel/coalescent:
GMRFSkylineLikelihood.java (+57 -18)
-
msuchard
2007-08-10 10:01
#25
Rev.: 481
-
879 lines of code changed in 5 files:
-
examples:
testGMRFCoalescent.xml (new 82)
-
src/dr/app/beastdev:
BeastParser.java (+9 -8)
-
src/dr/evomodel/coalescent:
GMRFSkylineLikelihood.java (+378 -376),
GMRFTestLikelihood.java (+172)
-
src/dr/evomodel/coalescent/operators:
GMRFSkylineBlockUpdateOperator.java (+238 -229)
-
rambaut
2007-08-10 02:50
#24
Rev.: 480
-
43 lines of code changed in 1 file:
-
src/dr/evomodel/treelikelihood:
AdvancedTreeLikelihood.java (+43 -10)
-
rambaut
2007-08-10 02:47
#23
Rev.: 478
-
9 lines of code changed in 2 files:
-
src/dr/app/tools:
TreeAnnotator.java (+7 -7)
-
src/dr/inference/model:
LogarithmStatistic.java (+2 -2)
-
rambaut
2007-08-09 01:25
#22
Rev.: 476
-
87 lines of code changed in 2 files:
-
src/dr/app/tools:
TreeAnnotator.java (+86 -24),
TreeAnnotatorDialog.java (+1 -1)
-
rambaut
2007-08-09 01:24
#21
Rev.: 475
-
1 lines of code changed in 1 file:
-
src/dr/inference/model:
LogarithmStatistic.java (+1 -1)
-
rambaut
2007-08-09 01:16
#20
Rev.: 473
-
374 lines of code changed in 14 files:
-
src/dr/app/beast:
BeastParser.java (+7 -4)
-
src/dr/app/beastdev:
BeastParser.java (+10 -9)
-
src/dr/inference/model:
DifferenceStatistic.java (+4 -2),
ExponentialStatistic.java (+92),
ExponentiationStatistic.java (del),
LogarithmStatistic.java (+108),
MeanStatistic.java (+24 -23),
NegateStatistic.java (del),
NegativeStatistic.java (+92),
NotStatistic.java (+9 -6),
ProductStatistic.java (+10 -4),
RatioStatistic.java (+4 -2),
ReciprocalStatistic.java (+6 -2),
SumStatistic.java (+8 -3)
-
alexei.drummond
2007-08-08 21:50
#19
Rev.: 469
-
1185 lines of code changed in 9 files:
-
src/dr/app/beastdev:
BeastMC3.java (+244 -239)
-
src/dr/evomodel/coalescent:
CoalescentSimulator.java (+91 -81)
-
src/dr/evomodel/tree:
TreeModelParser.java (+250 -225),
TreeTrace.java (new 137),
TreeTraceAnalysis.java (+208 -140)
-
src/dr/inference/mcmcmc:
MCMCMC.java (+96 -56)
-
src/dr/inference/model:
CompoundParameter.java (+3 -6)
-
src/dr/math:
GammaFunction.java (new)
-
jheled
2007-08-08 20:10
#18
Rev.: 468
-
275 lines of code changed in 6 files:
-
examples:
constrainedTaxaTest7.xml (new 1),
constrainedTaxaTest8.xml (new 98),
constrainedTaxaTest9.xml (new 102)
-
src/dr/app/beauti:
BeastGenerator.java (+5 -2)
-
src/dr/evolution/util:
Taxa.java (+9)
-
src/dr/evomodel/coalescent:
CoalescentSimulator.java (+60 -22)
-
alexei.drummond
2007-08-08 18:10
#17
Rev.: 467
-
139 lines of code changed in 2 files:
-
build_release.xml (+62 -61)
-
src/dr/evomodel/treelikelihood:
LikelihoodCore.java (+77 -71)
-
alexei.drummond
2007-08-07 20:59
#16
Rev.: 462
-
1039 lines of code changed in 11 files:
-
lib:
colt.jar (new)
-
src/dr/app/coalgen:
CoalGenApp.java (+4 -7),
CoalGenData.java (+142 -139),
CoalGenFrame.java (+270 -265),
CoalGenMenuFactory.java (+15 -17),
DataPanel.java (+473 -456),
ModelPanel.java (+135 -135),
Trace.java (del),
TraceException.java (del),
TraceList.java (del),
Traces.java (del)
-
msuchard
2007-08-07 08:37
#15
Rev.: 458
-
1017 lines of code changed in 4 files:
-
examples:
testGMRFCoalescent.xml (+90 -82)
-
src/dr/app/beastdev:
BeastParser.java (+204 -203)
-
src/dr/evomodel/coalescent:
GMRFSkylineLikelihood.java (+238 -168)
-
src/dr/evomodel/coalescent/operators:
GMRFSkylineBlockUpdateOperator.java (+485)
-
rambaut
2007-08-07 00:27
#14
Rev.: 454
-
0 lines of code changed in 1 file:
-
src/dr/inference/distribution:
UniformDistributionModel.java (-1)
-
rambaut
2007-08-07 00:26
#13
Rev.: 453
-
2 lines of code changed in 1 file:
-
src/dr/inference/model:
AbstractModel.java (+2 -2)
-
rambaut
2007-08-07 00:23
#12
Rev.: 452
-
62 lines of code changed in 42 files:
-
src/dr/app/beast:
BeastMain.java (+1 -1),
BeastParser.java (+2),
BeastVersion.java (+6 -14)
-
src/dr/app/beauti:
BeastGenerator.java (+11 -2),
BeautiFrame.java (-9),
BeautiOptions.java (+7 -1),
DataPanel.java (+6 -26),
MCMCPanel.java (+19 -1)
-
src/dr/evomodel/clock:
UniversalClock.java (+1 -8)
-
src/dr/evomodel/coalescent:
CoalescentLikelihood.java (-9),
EmpiricalPiecewiseModel.java (+1 -2),
PiecewisePopulationModel.java (+1 -2),
ScaledPiecewiseModel.java (+1 -2)
-
src/dr/evomodel/continuous:
DiffusionModel.java (+1 -2),
MultivariateDiffusionModel.java (-3),
MultivariateTraitLikelihood.java (-8),
TraitLikelihood.java (-8)
-
src/dr/evomodel/indel:
TKF91Likelihood.java (-4),
TKF91Model.java (+1 -4)
-
src/dr/evomodel/sitemodel:
CategorySiteModel.java (-3),
GammaSiteModel.java (-3),
SampleStateAndCategoryModel.java (-1),
SampleStateModel.java (-1)
-
src/dr/evomodel/speciation:
BranchingLikelihood.java (-6),
BranchingModel.java (+1 -2),
SpeciationLikelihood.java (-9),
SpeciationModel.java (+1 -2)
-
src/dr/evomodel/substmodel:
AbstractNucleotideModel.java (+1 -8),
AbstractSubstitutionModel.java (-1),
EmpiricalAminoAcidModel.java (-1),
FrequencyModel.java (-1),
GeneralSubstitutionModel.java (+1 -8),
HKY.java (-8),
PseudoCodonModel.java (-1)
-
src/dr/evomodel/transmission:
TransmissionLikelihood.java (-1)
-
src/dr/evomodel/tree:
TreeModel.java (-6),
UniformRootPrior.java (-8)
-
src/dr/inference/distribution:
ExponentialDistributionModel.java (-1),
ExponentialMarkovModel.java (-1),
GammaDistributionModel.java (-1),
LogNormalDistributionModel.java (-3),
NormalDistributionModel.java (-1)
-
rambaut
2007-08-07 00:12
#11
Rev.: 451
-
330 lines of code changed in 4 files:
-
src/dr/inference/model:
DifferenceStatistic.java (+119),
ProductStatistic.java (+87 -69),
RatioStatistic.java (+119),
SumStatistic.java (+5 -1)
-
alexei.drummond
2007-08-06 22:48
#10
Rev.: 450
-
40 lines of code changed in 2 files:
-
src/dr/app/beauti:
BeautiApp.java (+20 -3),
BeautiOptions.java (+20 -3)
-
alexei.drummond
2007-08-06 22:07
#9
Rev.: 449
-
1265 lines of code changed in 2 files:
-
src/dr/app/beauti:
BeautiApp.java (+12 -11),
BeautiOptions.java (+1253 -1229)
-
alexei.drummond
2007-08-06 20:16
#8
Rev.: 448
-
99 lines of code changed in 4 files:
-
src/dr/app/beast:
BeastParser.java (-1)
-
src/dr/app/beastdev:
BeastParser.java (-1)
-
src/dr/inference/loggers:
MCLogger.java (+1 -1)
-
src/dr/inference/trace:
Trace.java (+98)
-
alexei.drummond
2007-08-06 18:35
#7
Rev.: 447
-
4442 lines of code changed in 35 files:
-
src/dr/app/tools:
LogAnalyser.java (+92 -86)
-
src/dr/app/tracer/analysis:
BayesianSkylineDialog.java (+615 -587),
DemographicDialog.java (+475 -443),
MarginalLikelihoodDialog.java (new 114)
-
src/dr/app/tracer/application:
TracerApp.java (+75 -75),
TracerFrame.java (+712 -651)
-
src/dr/app/tracer/traces:
CombinedTraces.java (+159 -99),
CorrelationPanel.java (+20 -15),
DensityPanel.java (+177 -157),
FrequencyPanel.java (+62 -58),
IntervalsPanel.java (+6 -2),
LogFileTraces.java (del),
RawTracePanel.java (+202 -179),
SummaryStatisticsPanel.java (+215 -182),
Trace.java (del),
TraceCorrelation.java (del),
TraceDistribution.java (del),
TraceException.java (del),
TraceList.java (del),
TracePanel.java (+77 -60)
-
src/dr/evomodel/continuous:
BivariateDiscreteMapMaker.java (new 202)
-
src/dr/inference/distribution:
EmpiricalDistributionLikelihood.java (del)
-
src/dr/inference/loggers:
MCLogger.java (+191 -179)
-
src/dr/inference/trace:
BayesFactor.java (del),
DensityRectangle.java (+43 -43),
LogFileTraces.java (+341),
MarginalLikelihoodAnalysis.java (+70 -40),
Trace.java (del),
TraceAnalysis.java (+81 -328),
TraceAnalysisParser.java (+74 -70),
TraceCorrelation.java (+125),
TraceDistribution.java (+154),
TraceException.java (new 44),
TraceList.java (+112)
-
src/dr/math:
LogTricks.java (+4 -4)
-
alexei.drummond
2007-08-06 07:46
#6
Rev.: 446
-
352 lines of code changed in 8 files:
-
src/dr/app/beast:
BeastMain.java (+2 -2)
-
src/dr/app/tracer/traces:
LogFileTraces.java (new 4),
Trace.java (new 4),
TraceList.java (new 21)
-
src/dr/inference/loggers:
MCLogger.java (+9 -2),
TabDelimitedFormatter.java (+8 -7)
-
src/dr/inference/trace:
Trace.java (new 299),
TraceAnalysis.java (+5 -1)
-
jheled
2007-08-05 20:15
#5
Rev.: 445
-
922 lines of code changed in 16 files:
-
examples:
constrainedTaxaTest1.xml (new 75),
constrainedTaxaTest2.xml (new 76),
constrainedTaxaTest3.xml (new 92),
constrainedTaxaTest4.xml (new 94),
constrainedTaxaTest5.xml (new 112),
constrainedTaxaTest6.xml (new 78),
constrainedTaxaTest7.xml (+101)
-
src/dr/evolution/coalescent:
Coalescent.java (+6 -6),
CoalescentSimulator.java (+32 -28)
-
src/dr/evolution/tree:
SimpleNode.java (+1 -2),
Tree.java (+16)
-
src/dr/evolution/util:
Taxa.java (+22 -5)
-
src/dr/evomodel/coalescent:
CoalescentLikelihood.java (+4 -4),
CoalescentMRCALikelihood.java (new 35),
CoalescentSimulator.java (+109 -103),
VariableDemographicModel.java (+69 -45)
-
jheled
2007-08-05 20:13
#4
Rev.: 444
-
8 lines of code changed in 4 files:
-
src/dr/inference/operators:
BitFlipOperator.java (+3 -1),
BitSwapOperator.java (+1 -1),
ScaleOperator.java (+1 -1),
UniformOperator.java (+3 -1)
-
jheled
2007-08-05 20:12
#3
Rev.: 443
-
18 lines of code changed in 1 file:
-
src/dr/inference/trace:
TraceAnalysisParser.java (+18 -18)
-
jheled
2007-08-05 20:11
#2
Rev.: 442
-
2 lines of code changed in 1 file:
-
src/dr/xml:
ElementRule.java (+2 -2)
-
Sebastian.Hoehna
2007-08-01 02:42
#1
-
1080 lines of code changed in 12 files:
-
.classpath (+10 -8)
-
src/dr/app/beast:
BeastParser.java (+3)
-
src/dr/evolution/tree:
BranchScoreMetric.java (+159),
Clade.java (+41)
-
src/dr/evomodel/operators:
ColouredSubtreeSlideOperator.java (-12),
ECR.java (+192),
NNI.java (+206),
SPR.java (+253),
SubtreeSlideOperator.java (-12),
WilsonBalding.java (-10)
-
src/dr/evomodel/tree:
TreeMetricStatistic.java (+148 -105)
-
src/dr/inference/operators:
SimpleMCMCOperator.java (+68)