-
fbielejec
2012-09-28 21:06
#22
Rev.: 5178
-
133 lines of code changed in 1 file:
-
src/dr/app/beagle/tools:
BeagleSequenceSimulator.java (+133 -249)
-
msuchard
2012-09-27 21:22
#21
Rev.: 5177
-
104 lines of code changed in 3 files:
-
src/dr/app/beast:
development_parsers.properties (+1)
-
src/dr/evomodelxml:
LeafTraitExtractorParser.java (new 89)
-
src/dr/geo:
GeoSpatialDistribution.java (+14 -10)
-
tbcbedford@gmail.com
2012-09-27 00:36
#20
Rev.: 5176
-
2 lines of code changed in 1 file:
-
src/dr/evomodel/antigenic:
AntigenicLikelihood.java (+2 -1)
-
fbielejec
2012-09-24 21:54
#19
Rev.: 5175
-
162 lines of code changed in 1 file:
-
src/dr/app/beagle/tools:
BeagleSequenceSimulator.java (+162 -45)
-
rambaut
2012-09-19 03:38
#18
Rev.: 5174
-
0 lines of code changed in 2 files:
-
src/dr/evomodelxml/coalescent:
CoalescentSimulatorParser.java (-2)
-
fbielejec
2012-09-19 00:53
#17
Rev.: 5173
-
58 lines of code changed in 4 files:
-
src/dr/app/beagle/tools:
BeagleSequenceSimulator.java (+52 -30),
Partition.java (+1 -1)
-
src/dr/app/beagle/tools/parsers:
BeagleSequenceSimulatorParser.java (+3 -2),
PartitionParser.java (+2 -2)
-
fbielejec
2012-09-18 21:55
#16
Rev.: 5172
-
169 lines of code changed in 4 files:
-
src/dr/app/beagle/tools:
BeagleSequenceSimulator.java (+138 -10),
Partition.java (+2)
-
src/dr/app/beagle/tools/parsers:
BeagleSequenceSimulatorParser.java (+29 -2),
PartitionParser.java (-4)
-
fbielejec
2012-09-18 19:31
#15
Rev.: 5171
-
38 lines of code changed in 4 files:
-
src/dr/app/beagle/tools:
BeagleSequenceSimulator.java (+7 -5),
Partition.java (+5 -12)
-
src/dr/app/beagle/tools/parsers:
BeagleSequenceSimulatorParser.java (+18 -6),
PartitionParser.java (+8 -17)
-
Sibon.Li@gmail.com
2012-09-18 19:14
#14
Rev.: 5170
-
2 lines of code changed in 4 files:
-
src/dr/inference/markovchain:
MarkovChainDelegate.java (+1 -1)
-
src/dr/inference/mcmc:
MCMC.java (new)
-
Sibon.Li@gmail.com
2012-09-18 17:42
#13
Rev.: 5169
-
153 lines of code changed in 1 file:
-
src/dr/app/tracer/application:
InstantiableTracerApp.java (+153)
-
fbielejec
2012-09-18 02:30
#12
Rev.: 5168
-
20 lines of code changed in 2 files:
-
src/dr/app/beagle/tools:
BeagleSequenceSimulator.java (+3 -2)
-
src/dr/app/beagle/tools/parsers:
BeagleSequenceSimulatorParser.java (+17 -5)
-
fbielejec
2012-09-18 02:13
#11
Rev.: 5167
-
166 lines of code changed in 6 files:
-
src/dr/app/beagle/tools:
BeagleSequenceSimulator.java (+9 -9),
Partition.java (+4)
-
src/dr/app/beagle/tools/parsers:
BeagleSequenceSimulatorParser.java (+8 -86),
PartitionParser.java (+142 -2)
-
src/dr/app/beast:
beagle_parsers.properties (+3),
development_parsers.properties (-1)
-
fbielejec
2012-09-18 00:44
#10
Rev.: 5166
-
72 lines of code changed in 4 files:
-
src/dr/app/beagle/tools:
BeagleSequenceSimulator.java (-1),
Partition.java (+65)
-
src/dr/app/beagle/tools/parsers:
PartitionParser.java (+7)
-
src/dr/app/bss:
Partition.java (del)
-
fbielejec
2012-09-18 00:14
#9
Rev.: 5165
-
118 lines of code changed in 2 files:
-
src/dr/app/beagle/tools:
BeagleSequenceSimulator.java (+110 -38)
-
src/dr/app/bss:
Partition.java (new 8)
-
fbielejec
2012-09-17 20:11
#8
Rev.: 5164
-
59 lines of code changed in 1 file:
-
src/dr/app/bss:
Partition.java (+59)
-
fbielejec
2012-09-17 20:10
#7
Rev.: 5163
-
368 lines of code changed in 3 files:
-
src/dr/app/beagle/tools:
BeagleSequenceSimulator.java (+345 -339)
-
src/dr/app/beagle/tools/parsers:
BeagleSequenceSimulatorParser.java (+12 -9)
-
src/dr/app/bss:
BeagleSequenceSimulatorFrame.java (+11 -8)
-
graham853@gmail.com
2012-09-15 02:40
#6
Rev.: 5162
-
523 lines of code changed in 14 files:
-
src/dr/evolution/tree:
SlidableTree.java (+5 -6)
-
src/dr/evomodel/operators:
AlloppChangeNumHybridizations.java (+82 -25),
AlloppNetworkNodeSlide.java (+1 -1),
AlloppSequenceReassignment.java (+1)
-
src/dr/evomodel/speciation:
AlloppDiploidHistory.java (+79 -24),
AlloppLeggedTree.java (+3 -4),
AlloppMulLabTree.java (+22),
AlloppSpeciesBindings.java (+5 -11),
AlloppSpeciesNetworkModel.java (+153 -28),
PopsIOSpeciesTreeModel.java (+154 -102)
-
src/test/dr/evomodel/speciation:
AlloppSpeciesNetworkModelTEST.java (+18 -1)
-
rambaut
2012-09-13 08:04
#5
Rev.: 5155
-
1 lines of code changed in 1 file:
-
src/dr/inference/model:
CompoundLikelihood.java (+1 -1)
-
msuchard
2012-09-12 10:00
#4
-
267 lines of code changed in 7 files:
-
src/dr/app/beast:
release_parsers.properties (+1)
-
src/dr/evomodel/branchratemodel:
ArbitraryBranchRates.java (+17 -7)
-
src/dr/evomodelxml/branchratemodel:
ArbitraryBranchRatesParser.java (+32 -1)
-
src/dr/inference/distribution:
SkewNormalDistributionModel.java (new 152)
-
src/dr/inferencexml/distribution:
SkewNormalDistributionModelParser.java (new 65)
-
fbielejec
2012-09-11 19:41
#3
Rev.: 5151
-
45 lines of code changed in 4 files:
-
src/dr/app/beagle/evomodel/sitemodel:
EpochBranchSubstitutionModel.java (+36 -28)
-
src/dr/app/bss:
BeagleSequenceSimulatorApp.java (+8 -6),
BeagleSequenceSimulatorData.java (-3),
ExceptionHandler.java (+1 -1)
-
fbielejec
2012-09-07 02:06
#2
Rev.: 5150
-
135 lines of code changed in 6 files:
-
build_bss.xml (+125 -136)
-
src/dr/app/beagle/evomodel/parsers:
BeagleSubstitutionEpochModelParser.java (-2),
GammaSiteModelParser.java (+9 -4)
-
src/dr/app/beagle/tools:
BeagleSequenceSimulator.java (-23)
-
src/dr/app/beagle/tools/parsers:
BeagleSequenceSimulatorParser.java (-4)
-
src/dr/app/beast:
beagle_parsers.properties (+1)
-
graham853@gmail.com
2012-09-02 04:49
#1
Rev.: 5149
-
3294 lines of code changed in 39 files:
-
src/dr/app/beast:
development_parsers.properties (+3)
-
src/dr/evomodel/operators:
AlloppChangeNumHybridizations.java (+237),
AlloppHybPopSizesScale.java (new 52),
AlloppMoveLegs.java (+1 -1),
AlloppNetworkNodeSlide.java (+84 -79)
-
src/dr/evomodel/speciation:
AlloppDiploidHistory.java (+720 -560),
AlloppFootLinks.java (del),
AlloppLegLink.java (del),
AlloppLeggedTree.java (+449 -751),
AlloppMSCoalescent.java (new),
AlloppMulLabTree.java (+479 -487),
AlloppNetworkPrior.java (+81 -161),
AlloppNetworkPriorModel.java (new),
AlloppNode.java (+32 -128),
AlloppSpeciesBindings.java (+111 -167),
AlloppSpeciesNetworkModel.java (+604 -987),
AlloppTreeLeg.java (del),
MulMSCoalescent.java (+1 -1),
MulSpeciesBindings.java (new),
MulSpeciesTreeModel.java (new),
PopsIOMSCoalescent.java (new),
PopsIOSpeciesBindings.java (+1 -1)
-
src/dr/evomodelxml/operators:
AlloppChangeNumHybridizationsParser.java (+55),
AlloppHybPopSizesScaleParser.java (new 55)
-
src/dr/evomodelxml/speciation:
AlloppNetworkPriorModelParser.java (new),
AlloppSpeciesNetworkModelParser.java (+50 -26)
-
src/dr/util:
AlloppMisc.java (new)
-
src/test/dr/evomodel/speciation:
AlloppSpeciesNetworkModelTEST.java (+100 -415)