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msuchard 2013-01-17 09:56 Rev.: 5329

Fixed normalization of CTMC reference prior

31 lines of code changed in 2 files:

• src/dr/evomodel/MSSD: CTMCScalePrior.java (new)

msuchard 2012-11-28 10:34 Rev.: 5260

Incomplete implementation of multi-state stochastic Dollo under BEAGLE. Needs considerably more work.

82 lines of code changed in 2 files:

• src/dr/evomodel/MSSD: AbstractObservationProcess.java (new)

msuchard 2011-06-19 15:55 Rev.: 4044

Added (approx.) conditional reference prior for overall substitution rate scalar into BEAUti

23 lines of code changed in 1 file:

• src/dr/evomodel/MSSD: CTMCScalePrior.java (+23 -9)

msuchard 2010-04-09 07:25 Rev.: 3107

More Fixes to store/restore in ALSTreeLikelihood

68 lines of code changed in 3 files:

• src/dr/evomodel/MSSD: ALSTreeLikelihood.java (new), AbstractObservationProcess.java (+64 -18)

msuchard 2010-04-08 13:45 Rev.: 3105

Fixed store/restore in ALSTreeLikelihood

30 lines of code changed in 3 files:

• src/dr/evomodel/MSSD: AbstractObservationProcess.java (+16 -16), AnyTipObservationProcess.java (+14 -12)

msuchard 2010-04-08 13:03 Rev.: 3104

Optimizing stochastic Dollo model; should run 2 - 3x faster now

89 lines of code changed in 2 files:

• src/dr/evomodel/MSSD: AbstractObservationProcess.java (+23 -14), AnyTipObservationProcess.java (+66 -41)

msuchard 2010-04-08 11:12 Rev.: 3101

Intermediate fixed to stochastic Dollo; more to follow

41 lines of code changed in 1 file:

• src/dr/evomodel/MSSD: AnyTipObservationProcess.java (+41 -19)

dong.w.xie 2010-03-03 08:46 Rev.: 3012

Trunk refactoring: finish MSSD (split parsers).

10 lines of code changed in 7 files:

• src/dr/evomodel/MSSD: ALSTreeLikelihood.java (-109), AnyTipObservationProcess.java (-54), CTMCScalePrior.java (+4 -52), ExponentialBranchLengthTreePrior.java (new), SingleTipObservationProcess.java (+2 -54)

dong.w.xie 2010-02-23 09:35 Rev.: 2959

Trunk refactoring: finish tree likihood model (split parsers)..

7 lines of code changed in 1 file:

• src/dr/evomodel/MSSD: ALSTreeLikelihood.java (+7 -6)

rambaut 2009-08-20 07:59 Rev.: 2109

Merged in changes removing the use of STL vectors from the CPU implementation. Also removed a few try blocks round calls to functions that don't and needn't throw exceptions.

1 lines of code changed in 1 file:

• src/dr/evomodel/MSSD: ALSTreeLikelihood.java (+1 -1)

alexei.drummond 2009-07-19 14:30 Rev.: 1873

Parameter -> Variable, Act 2 -- this is probably the biggest change made to core BEAST in a few years. So I tagged revision 1870 for convenience. Parameter is now basically obsoleted and should be replaced by DoubleVariable or Variable<Double> where appropriate. We can now also develop some Variable<Integer> and Variable<Boolean> et cetera so should be nice in the future... I have also added a Variable<double[]> for vectors and matrices. See dr.inference.tutorial.Tutorial1 for a first peek at programmable BEAST MCMC...

10 lines of code changed in 3 files:

• src/dr/evomodel/MSSD: AbstractObservationProcess.java (+6 -5), CTMCScalePrior.java (+2 -5), ExponentialBranchLengthTreePrior.java (+2 -5)

jheled 2009-05-07 07:45 Rev.: 1687

code police

1 lines of code changed in 1 file:

• src/dr/evomodel/MSSD: ALSTreeLikelihood.java (+1 -1)

jheled 2009-04-20 09:10 Rev.: 1607

Continued Marc's refactorization. I wonder what other shared functionality we can pull off in there.

0 lines of code changed in 2 files:

• src/dr/evomodel/MSSD: CTMCScalePrior.java (-16), ExponentialBranchLengthTreePrior.java (-16)

jheled 2009-04-19 08:35 Rev.: 1598

add a nethod for getting a meaningfull name of a likelihood. more classes may benefit from overriding the default.

5 lines of code changed in 2 files:

• src/dr/evomodel/MSSD: CTMCScalePrior.java (+3 -3), ExponentialBranchLengthTreePrior.java (+2 -2)

alexander.alekseyenko 2008-12-12 01:57 Rev.: 1380

added an example of binary stochastic Dollo model, +some minor related bug fixes.

7 lines of code changed in 1 file:

• src/dr/evomodel/MSSD: AbstractObservationProcess.java (+7 -2)

alexander.alekseyenko 2008-11-28 04:33 Rev.: 1341

Massive refactoring of MSSD model specification. See new example file testMSSD.xml to appreciate the resulting simplifications.

94 lines of code changed in 4 files:

• src/dr/evomodel/MSSD: ALSTreeLikelihood.java (+41 -5), AbstractObservationProcess.java (+12 -9), AnyTipObservationProcess.java (+7 -5), SingleTipObservationProcess.java (+34 -26)

alexei.drummond 2008-11-27 21:21 Rev.: 1340

Moved ParameterChangeType -> Parameter.ChangeType

11 lines of code changed in 3 files:

• src/dr/evomodel/MSSD: AbstractObservationProcess.java (+1 -2), CTMCScalePrior.java (+5 -2), ExponentialBranchLengthTreePrior.java (+5 -2)

alexei.drummond 2008-11-27 13:08 Rev.: 1337

added variable size functionality to Parameter

42 lines of code changed in 3 files:

• src/dr/evomodel/MSSD: AbstractObservationProcess.java (+2 -1), CTMCScalePrior.java (+38 -31), ExponentialBranchLengthTreePrior.java (+2 -5)

alexander.alekseyenko 2008-11-25 04:43 Rev.: 1328

Fixed store/restore problems whith tree updates in MSSD observation process.

76 lines of code changed in 2 files:

• src/dr/evomodel/MSSD: AbstractObservationProcess.java (+10 -2), AnyTipObservationProcess.java (+66 -60)

rambaut 2008-10-25 05:52 Rev.: 1256

Alex and I have been experimenting with a path sampling approach to estimating marginal likelihoods. See eXML in examples/testPathSampling.xml. Not sure it works.

1 lines of code changed in 1 file:

• src/dr/evomodel/MSSD: ALSTreeLikelihood.java (+1 -1)

alexei.drummond 2008-10-22 10:56 Rev.: 1243

simulation of trees from piecewise linear populations

0 lines of code changed in 1 file:

• src/dr/evomodel/MSSD: ALSTreeLikelihood.java (-2)

alexander.alekseyenko 2008-08-23 05:03 Rev.: 1169

1) added Ferreira-Suchard prior on branch length/ctmc scale parameter
2) cleaned out priors for MSSD, xml example updated
3) Added an option to NewickParser to scale the tree to a specified total length

114 lines of code changed in 4 files:

• src/dr/evomodel/MSSD: CTMCScalePrior.java (+114), alsDefaultPrior.java (del), alsGammaPrior.java (del), alsPriorLambdaIntegrator.java (del)

alexei.drummond 2008-08-23 02:27 Rev.: 1168

refactoring of ALS stuff with Alex

352 lines of code changed in 4 files:

• src/dr/evomodel/MSSD: ALSTreeLikelihood.java (+63 -51), AbstractObservationProcess.java (+78 -67), ExponentialBranchLengthTreePrior.java (+164), alsPriorLambdaIntegrator.java (new 47)

alexander.alekseyenko 2008-08-23 00:32 Rev.: 1167

Gamma prior on death rate for MSSD model and some consistency changes.

229 lines of code changed in 4 files:

• src/dr/evomodel/MSSD: AbstractObservationProcess.java (+4), AnyTipObservationProcess.java (+2 -13), SingleTipObservationProcess.java (+1 -1), alsGammaPrior.java (new 222)

rambaut 2008-07-02 02:25 Rev.: 969

OK. Automatic scaling is now working. If the initial evaluation of the log likelihood returns -Inf then it turns on. It will impact performance but is better than not working at all. There are a number of improvements that could be made: one is to switch it off again once the tree is significantly improved. The other is to only rescale on certain nodes.

I tested it by comparing with the ArbitraryPrecisionLikelihoodCore (see ExperimentalTreeLikelihood) which is a form of GeneralLikelihoodCore that uses BigDecimal to a specified precision.

1 lines of code changed in 1 file:

• src/dr/evomodel/MSSD: ALSTreeLikelihood.java (+1 -1)

rambaut 2008-07-01 03:23 Rev.: 967

Am working on a partial likelihood scaling mechanism that will allow us to calculate likelihoods of very bad trees and very big trees. The aim is that this is dynamic and switches off if no longer needed. It is crude at the moment but compiles and runs (and shouldn't affect anything that doesn't explicitly ask for it).

3 lines of code changed in 1 file:

• src/dr/evomodel/MSSD: ALSTreeLikelihood.java (+3 -8)

rambaut 2008-06-21 06:01 Rev.: 963

Added the ability to force the use of a Java nucleotide core (rather than native) in order to assist debugging.

1 lines of code changed in 1 file:

• src/dr/evomodel/MSSD: ALSTreeLikelihood.java (+1 -1)

jheled 2008-06-05 20:25 Rev.: 937

Change method name to something I understand

4 lines of code changed in 1 file:

• src/dr/evomodel/MSSD: alsDefaultPrior.java (new 4)

jheled 2008-05-28 09:51 Rev.: 899

Move getParameter and replaceParameter to AbstractXMLObjectParser - now used by multiple parsers

Renamed getSocketChild

Added generic 'public <T> T getAttribute(String name, T defaultValue)' to XMLObject - some usages of getXXXXattribute replaced. Update usage in your code if possible so we can one day remove the numerous getXXXXattribute

8 lines of code changed in 3 files:

• src/dr/evomodel/MSSD: AnyTipObservationProcess.java (+2 -2), SingleTipObservationProcess.java (+2 -2), alsDefaultPrior.java (+4 -4)

rambaut 2008-05-27 11:38 Rev.: 896

Added a flag to TreeLikelihood to allow missing taxa (defaults to false so that missing taxa throw an exception). If true then missing taxa are given missing data at all sites.

2 lines of code changed in 1 file:

• src/dr/evomodel/MSSD: ALSTreeLikelihood.java (+2 -2)

alexander.alekseyenko 2008-04-07 22:11 Rev.: 806

Reorganized stuff into stochasticdollo.
'als' prefix stands for acquisition-loss-substitution, which is a synonym for multi-state stochastic Dollo. Hope this clarifies any confusion.
Had some trouble committing in the previous revisions...

1002 lines of code changed in 6 files:

• src/dr/evomodel/MSSD: ALSTreeLikelihood.java (+136), AbstractObservationProcess.java (+228), AnyTipObservationProcess.java (+156), SingleTipObservationProcess.java (+78), alsDefaultPrior.java (+219), alsPriorLambdaIntegrator.java (+185)