April 2012 Commit Log

Number of Commits:

12

Number of Active Developers:

7

jheled@gmail.com 2012-04-26 18:26 #12 Rev.: 4932

A terrible hack which disables 2d HPD for the dmv attribute (by name)

6 lines of code changed in 1 file:

• src/dr/app/tools: TreeAnnotator.java (+6 -2)

rambaut 2012-04-26 07:20 #11 Rev.: 4930

Demoted the non-beagle form of AncestralTreeLikelihood (parser now specifies BEAGLE is required).

24 lines of code changed in 1 file:

• src/dr/evomodelxml/treelikelihood: AncestralStateTreeLikelihoodParser.java (+24 -23)

rambaut 2012-04-21 00:32 #10 Rev.: 4928

Fixed an issue with local clocks not propogating rates down the entire clade.

1 lines of code changed in 2 files:

• src/dr/evomodel/branchratemodel: LocalClockModel.java (+1 -1)

msuchard 2012-04-20 09:52 #9 Rev.: 4926

Fixed issue 621: BEAUti now provides unbounded logPopSizes and an initial value on the correct scale.

50 lines of code changed in 4 files:

• src/dr/app/beauti/options: PartitionOptions.java (+13 -8), PartitionTreePrior.java (+9 -7)
• src/dr/app/beauti/types: PriorScaleType.java (new)

fbielejec 2012-04-16 23:27 #8 Rev.: 4925

attempt at fixing RC xml gen

19 lines of code changed in 2 files:

• src/dr/app/beauti/components/ancestralstates: AncestralStatesComponentGenerator.java (+6 -7)
• src/dr/app/beauti/generator: TreeLikelihoodGenerator.java (+13 -9)

dong.w.xie@gmail.com 2012-04-13 17:06 #7 Rev.: 4923

update *BEAST tutorial

1014 lines of code changed in 27 files:

• doc/tutorial/StarBEAST: STARBEAST.pdf (new), STARBEAST.tex (+66 -66), gopher.xml (new 948)
• doc/tutorial/StarBEAST/figures: BEAST.png (new), BEAUti_DataPartitions2.png (new), BEAUti_GuessTrait.png (new), BEAUti_MCMC.png (changed), BEAUti_Trait2.png (new), BEAUti_Tree.png (new), FigTree.png (new), ImportNexus.png (new), Tracer1.png (new), Tracer2.png (changed), TreeAnnotator.png (new)

sibon.li 2012-04-07 06:46 #6 Rev.: 4920

Added an interface for delegating tasks in the Markov Chain

143 lines of code changed in 4 files:

• src/dr/inference/markovchain: MarkovChain.java (+26), MarkovChainDelegate.java (+46)
• src/dr/inference/mcmc: MCMC.java (+55 -1)
• src/dr/inferencexml: MCMCParser.java (+16 -3)

rambaut 2012-04-05 20:56 #5 Rev.: 4919

Added a switch (mergeColumns="true/false") to specify whether every column should have a unique location or whether columns with the same strain should share locations (and share these locations with rows for that strain). Defaults to true.

20 lines of code changed in 1 file:

• src/dr/evomodel/antigenic: AntigenicLikelihood.java (+20 -7)

tbcbedford@gmail.com 2012-04-04 23:43 #4 Rev.: 4918

Changing datesParameter to virusDatesParameter to feed to AntigenicDistancePrior (along with virusLocations).

9 lines of code changed in 1 file:

• src/dr/evomodel/antigenic: AntigenicLikelihood.java (+9 -9)

rambaut 2012-04-04 23:02 #3 Rev.: 4917

3 lines of code changed in 1 file:

• src/dr/app/beauti/generator: BeastGenerator.java (+3 -2)

rambaut 2012-04-04 23:01 #2 Rev.: 4916

Added ability to extract the locations of viruses only or sera only.

48 lines of code changed in 1 file:

• src/dr/evomodel/antigenic: AntigenicLikelihood.java (+48)

tbcbedford@gmail.com 2012-04-03 23:47 #1 Rev.: 4915

This reversion fixes the bug in the likelihood calculation. Something is off in computeMeasurementLikelihood.

19 lines of code changed in 1 file:

• src/dr/evomodel/antigenic: AntigenicLikelihood.java (+19 -19)

March 2012 »