February 2009 Commit Log

Number of Commits:
47
Number of Active Developers:
5
rambaut 2009-02-28 00:10 Rev.: 1463

Created a 'BranchSiteModel' whose job is to provide an EigenDecomposition for any branch/category. HomogenousBranchSiteModel simply wraps a single SubstitutionModel and a FrequencyModel for all branches/sites.

0 lines of code changed in 2 files:

rambaut 2009-02-27 23:57 Rev.: 1462

Created a SiteRateModel and a GammaSiteRate model. This new interface just provides relative rates and proportions for sites (so has no reference to substmodels or frequencymodels.

0 lines of code changed in 2 files:

rambaut 2009-02-27 23:31 Rev.: 1461

Finished up the design of the newsubstmodel package. Not currently used. To be used by newtreelikelihood.

89 lines of code changed in 8 files:

msuchard 2009-02-27 13:57 Rev.: 1460

Suggestion on how to handle time-aware (epoch) substitution models by introducing a TreeBranchSubstitutionModel

241 lines of code changed in 2 files:

msuchard 2009-02-27 13:10 Rev.: 1459

Added support for sampling 0/1 entries in a DesignMatrix

10 lines of code changed in 1 file:

msuchard 2009-02-27 07:41 Rev.: 1458

Added support for sampling 0/1 entries in a DesignMatrix

22 lines of code changed in 2 files:

msuchard 2009-02-25 13:52 Rev.: 1457

Alignment returned from SequenceSimulator now takes its DataType from the FrequenceModel used to construct it

3 lines of code changed in 1 file:

higgs.ml 2009-02-25 12:38 Rev.: 1456

sequence simulator added

4 lines of code changed in 1 file:

higgs.ml 2009-02-25 11:20 Rev.: 1455

initial version

256 lines of code changed in 1 file:

higgs.ml 2009-02-25 11:15 Rev.: 1454

test file for sequence generator dr.app.SequenceSimulator

143 lines of code changed in 1 file:

msuchard 2009-02-25 09:49 Rev.: 1453

Island geography bits

473 lines of code changed in 6 files:

msuchard 2009-02-24 14:05 Rev.: 1452

Oops. I broke and have now fixed again my changes to Report.

1 lines of code changed in 1 file:

rambaut 2009-02-24 02:58 Rev.: 1451

Pathogen improvements

4 lines of code changed in 3 files:

rambaut 2009-02-24 01:40 Rev.: 1450

Small additions to Tracer

24 lines of code changed in 1 file:

alexei.drummond 2009-02-23 21:50 Rev.: 1449

geo

470 lines of code changed in 7 files:

msuchard 2009-02-23 20:40 Rev.: 1448

Oops. I broke and have now fixed my changes to Report.

1 lines of code changed in 1 file:

alexei.drummond 2009-02-23 16:59 Rev.: 1447

simulator for Pacific island hopping model - work in progress!

0 lines of code changed in 3 files:

msuchard 2009-02-23 09:33 Rev.: 1446

A Gibbs sampler operator for multivariate normal traits on the root, internal and external nodes on a tree. Old operator only worked on internal nodes.

224 lines of code changed in 1 file:

alexei.drummond 2009-02-21 14:59 Rev.: 1445

had some fun problems with svn

195 lines of code changed in 1 file:

alexei.drummond 2009-02-21 14:54

compute great circle distances for taxa with lat/long locations and provide as a statistic

110 lines of code changed in 2 files:

alexei.drummond 2009-02-21 14:46 Rev.: 1442

compute great circle distances for taxa with lat/long locations and provide as a statistic

4902 lines of code changed in 2 files:

rambaut 2009-02-21 11:03 Rev.: 1441

Fixed problem with ConvertAlignment not using the correct genetic code (it basically always converted with the Universal code even if specified otherwise in the parser). This would result in incorrect likelihoods for other genetic codes in Codon models.

200 lines of code changed in 3 files:

msuchard 2009-02-20 16:31 Rev.: 1440

Fixed some bugs in ComplexSubstitutionModel and MaskedParameter. Added "save to file" option in Report; should not break anything (crossing fingers)

90 lines of code changed in 6 files:

msuchard 2009-02-17 13:22 Rev.: 1439

Yang mito vertebrate codon example

1547 lines of code changed in 3 files:

msuchard 2009-02-16 09:31 Rev.: 1438

MaskedParameter now listens to changes in the 0/1 masking bit parameter.

73 lines of code changed in 3 files:

jheled 2009-02-16 08:03 Rev.: 1437

automatic code improvments (intellij)

73 lines of code changed in 17 files:

jheled 2009-02-16 07:54 Rev.: 1436

Fix the math - add missing terms for parameters assumed to be constant.

4 lines of code changed in 1 file:

jheled 2009-02-16 07:52 Rev.: 1435

Add ability to calculate the likelihood of a sub-range (from - to).

33 lines of code changed in 1 file:

rambaut 2009-02-14 07:26 Rev.: 1434

Pathogen improvements

10 lines of code changed in 3 files:

rambaut 2009-02-14 04:37 Rev.: 1433

Pathogen work.

34 lines of code changed in 4 files:

rambaut 2009-02-14 02:35 Rev.: 1432

Added a cutdown version of FigTree as a library to the BEAST lib folder (and as a consequence had to add the jam.jar library). This is so the program 'Path-O-Gen' can use it but it may be useful elsewhere. To get dr/app/pathogen/ to compile you will need to add figtreepanel.jar to your dependencies. To get Path-O-Gen to run, you will need to add jam.jar to the class path.

19 lines of code changed in 4 files:

jheled 2009-02-13 14:24

Sampling proportion added to Birth-Death, based on Tanja derivation. Not tested by simulation. Expressions are identical to the ones pre-change when the default proportion (1) is used.

116 lines of code changed in 6 files:

msuchard 2009-02-13 11:48 Rev.: 1429

GLMSubstitutionModel now ensures that regression yields to valid rate matrix through a 0/1 prior.

16 lines of code changed in 1 file:

rambaut 2009-02-13 04:54 Rev.: 1428

First version of 'Path-O-Gen' complete.

290 lines of code changed in 8 files:

rambaut 2009-02-11 22:36 Rev.: 1427

Work on Path-O-Gen

0 lines of code changed in 1 file:

rambaut 2009-02-11 22:29 Rev.: 1426

Work on Path-O-Gen

83 lines of code changed in 2 files:

rambaut 2009-02-11 05:22 Rev.: 1425

More development of Pathogen

384 lines of code changed in 8 files:

rambaut 2009-02-11 05:01 Rev.: 1424

Work on Path-O-Gen

2 lines of code changed in 1 file:

rambaut 2009-02-11 02:58 Rev.: 1423

More development of Pathogen

62 lines of code changed in 7 files:

rambaut 2009-02-10 22:23 Rev.: 1422

Work on Path-O-Gen

10 lines of code changed in 4 files:

rambaut 2009-02-10 10:25 Rev.: 1421

Created a simple GUI program for doing root-to-tip regressions for checking time structured nature of trees. For historical reasons it is called 'Path-O-Gen'.

1356 lines of code changed in 11 files:

rambaut 2009-02-06 02:32 Rev.: 1420

Fixed an issue with Tracer where an exception was being thrown when the 'Combined' trace file was selected on its own.

10 lines of code changed in 1 file:

msuchard 2009-02-05 09:50 Rev.: 1419

BSSVS may not actually work for the ComplexSubstitutionModel. Added check that CTMC graph remains connected.

75 lines of code changed in 3 files:

rambaut 2009-02-05 04:39 Rev.: 1418

Added a check to XMLParser so that any element that uses idref cannot have other attributes or content. This should reveal XML errors where a reference was used but not indended so the content was ignored.

4 lines of code changed in 1 file:

msuchard 2009-02-03 17:29 Rev.: 1417

Arbitrary masking of parameters; useful for applying random scan operators on fixed subsets of components in a parameter. ComplexSubstitutionModel now supports BSSVS via a GLM.

497 lines of code changed in 6 files:

msuchard 2009-02-03 13:59 Rev.: 1416

Working on generalized linear modeling of general substitution matrices

232 lines of code changed in 6 files:

msuchard 2009-02-02 14:27 Rev.: 1415

Marc is an idiot and committed some files that didn't compile earlier. Sorry!

28 lines of code changed in 3 files:

January 2009 »

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