January 2008 Commit Log

Number of Commits:

20

Number of Active Developers:

3

rambaut 2008-01-31 23:18 #20 Rev.: 675

Fixed Issue 35

43 lines of code changed in 1 file:

• src/dr/gui/chart: PDFPlot.java (+43 -37)

rambaut 2008-01-31 12:38 #19 Rev.: 673

Added a Lineages-Through-Time plot to Tracer

647 lines of code changed in 4 files:

• src/dr/app/tracer/analysis: LineagesThroughTimeDialog.java (+596)
• src/dr/app/tracer/application: AnalysisMenuFactory.java (+8), AnalysisMenuHandler.java (+2), TracerFrame.java (+41 -2)

jheled 2008-01-30 12:56 #18 Rev.: 672

remove incorrect assert after checking that serial samples work

1 lines of code changed in 1 file:

• src/dr/evomodel/coalescent: VDdemographicFunction.java (+1 -1)

jheled 2008-01-30 12:55 #17 Rev.: 671

add missing line

1 lines of code changed in 1 file:

• src/dr/inference/trace: VariableDemographicAnalysis.java (+1)

jen.tom 2008-01-30 11:32 #16 Rev.: 670

Just checking that Jen can commit to the repository. Changes are only cosmetic.

1 lines of code changed in 1 file:

• src/dr/evomodel/coalescent: GMRFSkylineLikelihood.java (+1)

jheled 2008-01-15 10:41 #15

variable demographic stuff

1663 lines of code changed in 22 files:

• src/dr/app/beast: BeastParser.java (+6 -2)
• src/dr/app/beastdev: BeastParser.java (+15 -5)
• src/dr/app/treestat: TreeStatData.java (new)
• src/dr/app/treestat/statistics: TMRCASummaryStatistic.java (+26 -23), TreeSummaryStatistic.java (+1 -1)
• src/dr/evolution/coalescent: Coalescent.java (+7 -8), DemographicFunction.java (+13 -2), LogisticGrowth.java (+69 -20), MultiLociTreeSet.java (+91), ScaledDemographic.java (+64)
• src/dr/evomodel/coalescent: CoalescentLikelihood.java (+116 -66), VDdemographicFunction.java (+398), VariableDemographicModel.java (+86 -67), VariableSkylineLikelihood.java (+10 -11)
• src/dr/evomodel/tree: TreeModel.java (-1)
• src/dr/exporters: CSVExporter.java (+160)
• src/dr/inference/trace: LogFileTraceExporter.java (+129), TraceAnalysis.java (+113 -114), TraceDistribution.java (+3 -16), VariableDemographicAnalysis.java (+320)
• src/dr/util: TabularData.java (+26)

jheled 2008-01-15 10:41 #14 Rev.: 665

add convienece reading

14 lines of code changed in 1 file:

• src/dr/inference/trace: LogFileTraces.java (+14)

jheled 2008-01-15 10:38 #13

cleanup

37 lines of code changed in 2 files:

• src/dr/app/tracer/application: TracerFrame.java (+4 -6)
• src/dr/evolution/io: NexusImporter.java (+33 -31)

jheled 2008-01-15 10:33 #12 Rev.: 662

198 lines of code changed in 1 file:

• src/dr/evomodel/operators: NNI.java (+198 -200)

jheled 2008-01-15 10:30 #11 Rev.: 661

comment addition

1 lines of code changed in 1 file:

• src/dr/stats: DiscreteStatistics.java (+1)

jheled 2008-01-15 10:29 #10 Rev.: 660

123 lines of code changed in 1 file:

• src/dr/evolution/tree: CladeMetric.java (+123 -123)

jheled 2008-01-15 10:29 #9 Rev.: 659

add consistency check

42 lines of code changed in 1 file:

• src/dr/evolution/tree: Clade.java (+42 -41)

jheled 2008-01-15 10:28 #8 Rev.: 658

java 5

19 lines of code changed in 1 file:

• src/dr/app/treestat: CharactersPanel.java (+19 -17)

jheled 2008-01-15 10:27 #7 Rev.: 657

159 lines of code changed in 2 files:

• src/dr/evolution/tree: BranchScoreMetric.java (+159 -159)

jheled 2008-01-15 10:26 #6 Rev.: 656

correct name for array

6 lines of code changed in 1 file:

• src/dr/xml: AttributeRule.java (+6 -2)

rambaut 2008-01-15 01:32 #5 Rev.: 655

Added a default lower bound on substitution relative rate parameters of 1.0E-6 in BEAUti.

24 lines of code changed in 1 file:

• src/dr/app/beauti: BeautiOptions.java (+24 -24)

rambaut 2008-01-15 01:29 #4 Rev.: 654

Better reporting of errors in MarkovChain

2 lines of code changed in 1 file:

• src/dr/inference/markovchain: MarkovChain.java (+2)

rambaut 2008-01-15 01:24 #3 Rev.: 653

Fixed a problem with TreeAnnotator (BEAST 1.5 version) which meant it used too much memory. When counting the number of traits to summarize it was counting them from each node as different rather than the same trait and thus allocating arrays that were massive.

9 lines of code changed in 1 file:

• src/dr/app/tools: TreeAnnotator.java (+9 -9)

rambaut 2008-01-09 12:21 #2 Rev.: 652

Various improvements to BEAUti and the odd bit of cleaning up. Some additions to tracer

1396 lines of code changed in 19 files:

• build_release.xml (+1 -1), tracer_release.xml (+2 -2)
• examples: testMC3.xml (+301)
• src/dr/app/beast: BeastParser.java (+2 -1)
• src/dr/app/beastdev: BeastMC3.java (new 239)
• src/dr/app/beauti: BeastGenerator.java (+5 -5), BeautiApp.java (+9 -2), BeautiFrame.java (+2 -2), DataPanel.java (+23 -5), ModelPanel.java (+348 -338), PriorDialog.java (+2 -2), PriorsPanel.java (+17 -4)
• src/dr/app/tools: DensityMap.java (+21 -10)
• src/dr/app/tracer/analysis: DemographicDialog.java (+72 -5)
• src/dr/evolution/coalescent: ConstExpConst.java (new 146)
• src/dr/evomodel/branchratemodel: RandomLocalClockModel.java (+2 -1)
• src/dr/evomodel/coalescent: ConstExpConstModel.java (+197)
• src/dr/inference/mcmcmc: MCMCMC.java (+3 -4), MCMCMCRunner.java (+4 -1)

rambaut 2008-01-05 03:18 #1 Rev.: 651

Tracer tweaks

14 lines of code changed in 2 files:

• src/dr/app/beauti: BeastGenerator.java (+13)
• src/dr/stats: DiscreteStatistics.java (+1 -1)

December 2007 »