Directory src/dr/evomodel/treelikelihood/

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rambaut 2012-05-17 20:47 Rev.: 4979

Fix for issue with multi-threading not working. The issue was that -threads 0 was being treated as no-multithreading where as it should specify an automatic thread pool size (having no -threads option gives a thread 0 value). For best performance the default should be not to use the thread command line option (but -threads 1 should be used to turn off multithreading). This also affected -beagle_instances as these use the threadpool.

7 lines of code changed in 2 files:

• src/dr/evomodel/treelikelihood: TreeLikelihood.java (+7)

rambaut 2012-03-05 23:49 Rev.: 4770

Made full set of scaling options available to command line.

0 lines of code changed in 1 file:

• src/dr/evomodel/treelikelihood: TreeLikelihood.java (-1)

rambaut 2011-11-16 05:15 Rev.: 4433

Ported sequence error models to BeagleTreeLikelihood and implemented a variant model that emits tip states rather than tip partials.

216 lines of code changed in 11 files:

• src/dr/evomodel/treelikelihood: EpochTreeLikelihood.java (+5 -5), HypermutantErrorModel.java (new), NodePosteriorTreeLikelihood.java (new), SequenceErrorModel.java (+13 -2), TipPartialsModel.java (del), TipStatesModel.java (new 172), TreeLikelihood.java (+11 -11)

rambaut 2011-08-20 03:58 Rev.: 4216

Various bits

27 lines of code changed in 1 file:

• src/dr/evomodel/treelikelihood: TipPartialsModel.java (new 27)

dong.w.xie 2011-08-19 15:40 Rev.: 4213

trunk: merge from branch 1.6

8 lines of code changed in 2 files:

• src/dr/evomodel/treelikelihood: NativeNucleotideLikelihoodCore.java (new)

rambaut 2011-07-23 04:00 Rev.: 4116

uncommitting an erroneous revision

0 lines of code changed in 1 file:

• src/dr/evomodel/treelikelihood: EpochTreeLikelihood.java (changed)

sibon.li 2011-06-21 12:46 Rev.: 4053

Transferring my changes from branch 1.6 to trunk:

Changes to LogNormalDistributionModel to allow for the stdev value to also not
be in log space (r3774)
Changes to UncorrelatedRelaxedClockTest due to changes in
LogNormalDistributionModel in r3774 (r3775)
Minor change in MixtureModelBranchRates to fix an issue caused by changes in
revision 3735 (r3773)
Bug fix for AncestralSequenceAnnotator plus added a window to select
input/output files (r3819)
Fixed spelling for GeneralSubstitutionModelTest (r3833)
Fixed a RuntimeException for AncestralStateTreeLikelihood (r3957)

5 lines of code changed in 2 files:

• src/dr/evomodel/treelikelihood: AncestralStateTreeLikelihood.java (+5 -3)

rambaut 2011-04-20 20:49 Rev.: 3939

First part of a fix for issue 436 (http://code.google.com/p/beast-mcmc/issues/detail?id=436): This will prevent a TipPartialsModel being reused for different PatternLists.

7 lines of code changed in 1 file:

• src/dr/evomodel/treelikelihood: TipPartialsModel.java (+7)

msuchard 2011-01-26 09:54 Rev.: 3778

Fixing bug in ancestral state reconstruction when using ambiguities

9 lines of code changed in 1 file:

• src/dr/evomodel/treelikelihood: AncestralStateTreeLikelihood.java (+9)

dong.w.xie 2010-10-04 10:56 Rev.: 3596

Trunk: @Override is JDK1.6 code.

11 lines of code changed in 2 files:

• src/dr/evomodel/treelikelihood: HiddenLinkageLikelihood.java (new)

aaron.darling 2010-10-02 15:24 Rev.: 3594

Allow the use of a native general likelihood core. Change handling of TipPartialsModel change events so only affected nodes with TipPartialsModels get marked dirty -- saves lots of recompute.
---------------
Adding a new model of hidden linkage among reads in a metagenomic dataset. The model and its application to metagenomic datasets is described in a manuscript in preparation by Aaron Darling and Jonathan Eisen. This is one part of commit phase 2.

16 lines of code changed in 1 file:

• src/dr/evomodel/treelikelihood: TreeLikelihood.java (+16 -4)

aaron.darling 2010-10-02 15:16 Rev.: 3592

Warn the user when the native general likelihood core could not be loaded.

1 lines of code changed in 2 files:

• src/dr/evomodel/treelikelihood: NativeGeneralLikelihoodCore.java (+1)

aaron.darling 2010-10-02 15:11 Rev.: 3588

Adding a new model of hidden linkage among reads in a metagenomic dataset. The model and its application to metagenomic datasets is described in a manuscript in preparation by Aaron Darling and Jonathan Eisen. This is commit phase 1: adding new files. Phase 2 comes next, committing related changes to existing files.

111 lines of code changed in 1 file:

• src/dr/evomodel/treelikelihood: HiddenLinkageLikelihood.java (+111)

rambaut 2010-09-02 02:22 Rev.: 3480

Fixed a few issues with SequenceErrorModel. Also added an automatic dimension setting for the popsize parameter in GMRF.

26 lines of code changed in 1 file:

• src/dr/evomodel/treelikelihood: SequenceErrorModel.java (+26)

rambaut 2010-09-02 01:35 Rev.: 3479

Added an optional indicator parameter into the sequence error model to try to identify damaged sequences.

111 lines of code changed in 1 file:

• src/dr/evomodel/treelikelihood: SequenceErrorModel.java (+111 -56)

rambaut 2010-08-20 04:13 Rev.: 3414

Added command line option '-prefix <PREFIX>' to specify a string which will be prefixed to all output log files. This is an alternative to changing the log file names in the XML when running multiple replicate runs in the same location.

0 lines of code changed in 1 file:

• src/dr/evomodel/treelikelihood: NativeNucleotideLikelihoodCore.java (-3)

dong.w.xie 2010-08-16 11:19 Rev.: 3393

Trunk: solve Issue 357: window's programmer has broken compatibility with unix-based operating systems

4 lines of code changed in 1 file:

• src/dr/evomodel/treelikelihood: NativeNucleotideLikelihoodCore.java (+4 -1)

akaruiws 2010-06-18 18:45 Rev.: 3275

Importance sampling for the msat ancestral states.

8 lines of code changed in 2 files:

• src/dr/evomodel/treelikelihood: MicrosatelliteSamplerTreeLikelihood.java (+8 -47)

msuchard 2010-06-14 14:20 Rev.: 3264

DiscreteTraitBranchRateModel now works again for ancestral state reconstructions. Something is still wrong with AncestralStateBeagleTreeLikelihood however.

2 lines of code changed in 1 file:

• src/dr/evomodel/treelikelihood: AncestralStateTreeLikelihood.java (+2 -2)

rambaut 2010-06-07 23:07 Rev.: 3235

Simplified TreeTrait interface to remove explicit dimensionality. If multidimensional traits are required then it needs to use double[] as the type.

10 lines of code changed in 2 files:

• src/dr/evomodel/treelikelihood: AncestralStateTreeLikelihood.java (+5 -13), NodePosteriorTreeLikelihood.java (+5 -8)

akaruiws 2010-06-06 22:12 Rev.: 3233

Misc changes to classes for msat likelihood calculation.

60 lines of code changed in 1 file:

• src/dr/evomodel/treelikelihood: MicrosatelliteSamplerTreeLikelihood.java (+60 -18)

msuchard 2010-06-06 04:51 Rev.: 3229

Added an ascertainment correction unit test.

14 lines of code changed in 1 file:

• src/dr/evomodel/treelikelihood: TreeLikelihood.java (+14)

rambaut 2010-06-02 23:10 Rev.: 3216

In the interests of generalization, AncestralState has been improved to optionally take a trait name, renamed AncestralTrait, moved to dr.evomodel.tree. It has a parser synonym of AncestralState and defaults to getting the 'state' trait so it is backwards compatible with existing XML (namely testAncestralSequenceReconstuction.xml).

0 lines of code changed in 1 file:

• src/dr/evomodel/treelikelihood: AncestralState.java (del)

rambaut 2010-06-02 22:53 Rev.: 3215

TreeTraits commit number 2. This one is a bit more wide ranging with potential to break things. 1) BranchAttributeProvider and NodeAttributeProvider have been deleted and replaced with a combination of TreeTraits and TreeTraitProviders. Sources implement TreeTraitProvider to say that they can provide information about nodes and branches. A good example of a class which has been generalized is AncestralState (in evomodel.treelikelihood) - this now just takes a TreeTrait and logs the trait for a given MRCA (the trait can be anything at all - whereas previously it took an AncestralStateTreeLikelihood).

199 lines of code changed in 3 files:

• src/dr/evomodel/treelikelihood: AncestralState.java (new 126), AncestralStateTreeLikelihood.java (+42 -29), NodePosteriorTreeLikelihood.java (+31 -11)

rambaut 2010-06-02 00:12 Rev.: 3207

This update does a number of things. 1) TreeLoggerParser and DemographicLoggerParser were in dr.inferencexml which breaks the dependency rules as they link to things in dr.evomodel. These are now moved to dr.evomodelxml. 2) A dr.evolution.tree.TreeTrait interface is created which is a general purpose interface for access to traits on nodes/branches. BranchAttributeProvider and NodeAttributeProvider will be replaced by this interface in the next update. 3) All BranchRateModels now have a common abstract base class AbstractBranchRateModel to implement their common features (these now implement TreeTrait to provide rates).

24 lines of code changed in 2 files:

• src/dr/evomodel/treelikelihood: AncestralState.java (+1 -4), AncestralStateTreeLikelihood.java (+23 -6)

msuchard 2010-05-28 07:23 Rev.: 3194

Fixed bug in ascertainment correction (miscounted) and implemented in BEAGLE. Genomic-wide SNPs here we come!

5 lines of code changed in 1 file:

• src/dr/evomodel/treelikelihood: TreeLikelihood.java (+5 -23)

msuchard 2010-05-21 10:55 Rev.: 3176

Keeping AncestralState(Beagle)TreeLikelihoods up-to-date

15 lines of code changed in 1 file:

• src/dr/evomodel/treelikelihood: AncestralStateTreeLikelihood.java (+15 -14)

rambaut 2010-05-21 03:09 Rev.: 3174

Tweak to the hypermutant model

22 lines of code changed in 1 file:

• src/dr/evomodel/treelikelihood: HypermutantErrorModel.java (+22 -6)

rambaut 2010-04-23 22:30 Rev.: 3131

More work on the hypermutation model.

91 lines of code changed in 2 files:

• src/dr/evomodel/treelikelihood: HypermutantErrorModel.java (+90 -99), TipPartialsModel.java (+1 -1)

rambaut 2010-04-22 23:12 Rev.: 3130

Created an HypermutantAlignment that flags hypermutation contexts for use in the APOBECErrorModel. It does this by replacing 'A's by an ambiguity code for A/G if it is in the correct context in the alignment. These can then be compressed into unique site patterns so that speed is not affected.

Extracted a common abstract base class with ConvertAlignment which wraps an alignment.

263 lines of code changed in 2 files:

• src/dr/evomodel/treelikelihood: APOBECErrorModel.java (del), HypermutantErrorModel.java (+263)

rambaut 2010-04-15 08:40 Rev.: 3122

Minor tweaks to APOBEC model.

40 lines of code changed in 3 files:

• src/dr/evomodel/treelikelihood: APOBECErrorModel.java (new 32), SequenceErrorModel.java (+4), TipPartialsModel.java (+4)

rambaut 2010-04-13 11:03 Rev.: 3113

Added a few models of sequence (tip) error to model the action of hypermutation by APOBEC editing in HIV.

16 lines of code changed in 2 files:

• src/dr/evomodel/treelikelihood: APOBECErrorModel.java (+8 -2), SequenceErrorModel.java (+8 -1)

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

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

20 lines of code changed in 6 files:

• src/dr/evomodel/treelikelihood: AncestralState.java (-52), AncestralStateTreeLikelihood.java (-81), EpochTreeLikelihood.java (+11 -14), NodePosteriorTreeLikelihood.java (+5 -4), SequenceErrorModel.java (+2 -87), TreeLikelihood.java (+2 -82)

alexei.drummond 2010-01-27 12:34 Rev.: 2846

Marc and Alexei added joint likelihood calculation and test for ancestral state likelihood

24 lines of code changed in 1 file:

• src/dr/evomodel/treelikelihood: AncestralStateTreeLikelihood.java (+24 -11)

msuchard 2010-01-25 13:43 Rev.: 2834

Working on integrating out Brownian diffusion internal node traits

18 lines of code changed in 1 file:

• src/dr/evomodel/treelikelihood: AncestralStateTreeLikelihood.java (+18 -26)

alexei.drummond 2010-01-22 11:29 Rev.: 2830

Marc and Alexei added discrete trait based branch rate model - yay

97 lines of code changed in 3 files:

• src/dr/evomodel/treelikelihood: AbstractTreeLikelihood.java (new), AncestralStateTreeLikelihood.java (+93 -21)

msuchard 2009-12-10 05:36 Rev.: 2673

MarkovJumps now supports Markov reward processes. Also a typo fix in BeastMain and some unnecessary casting in AMTL.

10 lines of code changed in 1 file:

• src/dr/evomodel/treelikelihood: AncestralStateTreeLikelihood.java (+10 -9)

msuchard 2009-11-27 08:43 Rev.: 2620

Smashing bugs in MarkovJumps

5 lines of code changed in 1 file:

• src/dr/evomodel/treelikelihood: AncestralStateTreeLikelihood.java (+5 -1)

jheled 2009-10-28 11:26 Rev.: 2480

Have name of likelihood or tree in info message when there are several of those.

13 lines of code changed in 1 file:

• src/dr/evomodel/treelikelihood: TreeLikelihood.java (+13 -9)

rambaut 2009-10-27 02:01 Rev.: 2473

Implemented an empirical tree distribution model and operator.

0 lines of code changed in 1 file:

• src/dr/evomodel/treelikelihood: TreeLikelihood.java (-3)

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