Directory src/dr/evomodel/substmodel/

Total Files:
54
Deleted Files:
6
Lines of Code:
6390

[root]/src/dr/evomodel/substmodel

Lines of Code

src/dr/evomodel/substmodel/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
Totals 412 (100.0%) 18652 (100.0%) 45.2
alexei.drummond 81 (19.7%) 6122 (32.8%) 75.5
msuchard 85 (20.6%) 6046 (32.4%) 71.1
rambaut 66 (16.0%) 2744 (14.7%) 41.5
akaruiws 55 (13.3%) 2064 (11.1%) 37.5
jheled 46 (11.2%) 654 (3.5%) 14.2
dong.w.xie 66 (16.0%) 348 (1.9%) 5.2
baele.guy@gmail.com 3 (0.7%) 330 (1.8%) 110.0
alexander.alekseyenko 4 (1.0%) 308 (1.7%) 77.0
fbielejec 2 (0.5%) 31 (0.2%) 15.5
Michael.DefoinPLatel 4 (1.0%) 5 (0.0%) 1.2

Most Recent Commits

baele.guy@gmail.com 2013-04-10 01:45 Rev.: 5570

Added LG model to the available types.

1 lines of code changed in 2 files:

  • src/dr/evomodel/substmodel: AminoAcidModelType.java (new)
baele.guy@gmail.com 2013-04-10 01:44 Rev.: 5569

Added the LG model of amino acid evolution (Le and Gascuel, 2008).

329 lines of code changed in 1 file:

  • src/dr/evomodel/substmodel: LG.java (new 329)
akaruiws 2013-02-19 16:32 Rev.: 5433

Modify to handle ambiguity.

3 lines of code changed in 2 files:

  • src/dr/evomodel/substmodel: MicrosatelliteModel.java (new)
rambaut 2012-08-08 10:19 Rev.: 5107

Porting 'evaluateLate' interface method from 1.7 branch.

16 lines of code changed in 6 files:

  • src/dr/evomodel/substmodel: ComplexSubstitutionModel.java (new), MultivariateOUModel.java (new), SVSGeneralSubstitutionModel.java (+8)
fbielejec 2012-06-12 23:42 Rev.: 5034

cleaning code

31 lines of code changed in 2 files:

  • src/dr/evomodel/substmodel: SubstitutionEpochModel.java (new)
rambaut 2012-03-13 03:10 Rev.: 4826

Fixed issue with date parameter

5 lines of code changed in 1 file:

  • src/dr/evomodel/substmodel: MultivariateOUModel.java (+5)
msuchard 2012-03-08 07:09 Rev.: 4789

Implemented TN93 under BEAGLE.

19 lines of code changed in 2 files:

  • src/dr/evomodel/substmodel: TN93.java (+19 -19)
dong.w.xie 2011-11-24 11:00 Rev.: 4481

trunk:solve Issue 457: BEAST should raise an error if binary dataType set but data is not binary, and Issue 312: BEAST continues to run (inappropriately) when sequence contains invalid character

15 lines of code changed in 5 files:

  • src/dr/evomodel/substmodel: ComplexSubstitutionModel.java (+5), PositiveDefiniteSubstitutionModel.java (+5), SVSComplexSubstitutionModel.java (+5)
rambaut 2011-11-15 05:14 Rev.: 4423

Added citations to amino acid models and a text box in BEAUti.

186 lines of code changed in 17 files:

  • src/dr/evomodel/substmodel: AminoAcidModelType.java (+24 -10), Blosum62.java (new), CPREV.java (new), Dayhoff.java (+23), EmpiricalRateMatrix.java (+2 -1), FLU.java (new), JTT.java (+22), MTREV.java (new), WAG.java (new)
dong.w.xie 2011-07-07 17:02 Rev.: 4102

GF81

118 lines of code changed in 1 file:

  • src/dr/evomodel/substmodel: GeneralF81Model.java (new 118)
akaruiws 2011-04-01 01:16 Rev.: 3911

Tidy up MsatBMA related things.

243 lines of code changed in 4 files:

  • src/dr/evomodel/substmodel: MsatAveragingSubsetModel.java (del), MsatBMA.java (new 238), TwoPhaseModel.java (new)
msuchard 2011-03-02 12:15 Rev.: 3844

Amino acid substitution model for influenza.

166 lines of code changed in 1 file:

  • src/dr/evomodel/substmodel: FLU.java (+166)
akaruiws 2011-02-17 15:37 Rev.: 3806

BMA for nucleotide substition models and gamma site model.

14 lines of code changed in 2 files:

  • src/dr/evomodel/substmodel: NtdBMA.java (+14 -8)
akaruiws 2011-02-15 14:01 Rev.: 3799

Handle the variable change more efficiently.

27 lines of code changed in 1 file:

  • src/dr/evomodel/substmodel: NtdBMA.java (+27)
akaruiws 2011-02-15 13:00 Rev.: 3798

Model averaging for nucleotide models.

83 lines of code changed in 1 file:

  • src/dr/evomodel/substmodel: NtdBMA.java (+83)
rambaut 2011-01-24 23:18 Rev.: 3777

Some new empirical codon models by Stefan Zoller (ETH Zurich) & Adrian Schneider (U. of Edinburgh). Example files in examples/release/EmpiricalCodonModels

1044 lines of code changed in 5 files:

  • src/dr/evomodel/substmodel: AbstractPCARateMatrix.java (new 64), EmpiricalCodonModel.java (new 603), EmpiricalCodonRateMatrix.java (new 105), PCACodonModel.java (new 149), PCARateMatrixMammalia.java (new 123)
akaruiws 2010-09-25 18:02 Rev.: 3572

updates for watkins msat model classes.

63 lines of code changed in 2 files:

  • src/dr/evomodel/substmodel: NewMicrosatelliteModel.java (+63 -15)
msuchard 2010-09-15 07:58 Rev.: 3540

Fixed ComplexSubstitutionModel so that pi parameter does post-multiply the rates parameter.

7 lines of code changed in 1 file:

  • src/dr/evomodel/substmodel: ComplexSubstitutionModel.java (+7 -3)
akaruiws 2010-09-08 10:06 Rev.: 3505

Added methods for computing the transition probabilities.

7 lines of code changed in 1 file:

  • src/dr/evomodel/substmodel: NewMicrosatelliteModel.java (+7 -2)
akaruiws 2010-09-08 09:52 Rev.: 3504

Added methods for computing the transition probabilities.

35 lines of code changed in 1 file:

  • src/dr/evomodel/substmodel: NewMicrosatelliteModel.java (+35)
akaruiws 2010-09-08 00:43 Rev.: 3503

New msat model described by Watkins (2007).

22 lines of code changed in 1 file:

  • src/dr/evomodel/substmodel: NewMicrosatelliteModel.java (+22)
rambaut 2010-08-05 04:21 Rev.: 3365

These models now allow a null indicator parameter in the constructor in which case they create one full of ones.

8 lines of code changed in 1 file:

  • src/dr/evomodel/substmodel: SVSComplexSubstitutionModel.java (+8 -5)
rambaut 2010-07-28 05:02 Rev.: 3325

Cleaned up the GeneralSubstitutionModel parser even more. This involved getting rid of SVSIrreversibleSubstModel (old code, Marc promises me). RootFreqs are gone - only worked with the old Irreversible model. Can be done other ways now. svsComplexSubstitutionModel and svsGeneralSubstitutionModel are synonyms of this parser and should allow backwards compatibility.

4 lines of code changed in 3 files:

  • src/dr/evomodel/substmodel: SVSComplexSubstitutionModel.java (+4 -4), SVSGeneralSubstitutionModel.java (-124), SVSIrreversibleSubstitutionModel.java (del)
rambaut 2010-07-23 03:01 Rev.: 3321

Cleaned up GeneralSubstitutionModelParser so it generally uses SVSGeneralSubstitutionModel or SVSIrreversibleSubstitutionModel (creating indicators = 1 if not specified). The only case now where it will use GeneralSubstitutionModel is if relativeTo attribute is specified.

7 lines of code changed in 1 file:

  • src/dr/evomodel/substmodel: SVSGeneralSubstitutionModel.java (+7 -3)
akaruiws 2010-07-01 17:32 Rev.: 3298

Gibbs sampling for a single msat ancestral state.

56 lines of code changed in 1 file:

  • src/dr/evomodel/substmodel: MicrosatelliteModel.java (+56)
akaruiws 2010-06-18 18:45 Rev.: 3275

Importance sampling for the msat ancestral states.

48 lines of code changed in 1 file:

  • src/dr/evomodel/substmodel: MicrosatelliteModel.java (+48 -2)
akaruiws 2010-06-11 12:47 Rev.: 3248

Msat model averaging.

214 lines of code changed in 1 file:

  • src/dr/evomodel/substmodel: MsatAveragingSubsetModel.java (new 214)
akaruiws 2010-06-06 16:23 Rev.: 3230

Misc changes to msat models.

201 lines of code changed in 8 files:

  • src/dr/evomodel/substmodel: AsymmetricQuadraticModel.java (+40 -36), LinearBiasModel.java (new), MicrosatelliteModel.java (+78 -8), OnePhaseModel.java (+7 -17), TwoPhaseModel.java (+38 -22)
dong.w.xie 2010-04-13 18:04 Rev.: 3117

TRUNK: sovle Issue 300: have a single parser 'generalSubstitutionModel' and get rid of 'svsGeneralSubstitutionModel' paser

8 lines of code changed in 1 file:

  • src/dr/evomodel/substmodel: SVSGeneralSubstitutionModel.java (+8 -7)
dong.w.xie 2010-04-12 11:12 Rev.: 3112

TRUNK: sovle Issue 295: If no BSSVS then no need for the indicators parameter

2 lines of code changed in 1 file:

  • src/dr/evomodel/substmodel: SVSGeneralSubstitutionModel.java (+2 -2)
dong.w.xie 2010-03-03 10:42 Rev.: 3013

Trunk refactoring: finish MULTIVARIATE OU PROCESS (split parsers).

7 lines of code changed in 2 files:

  • src/dr/evomodel/substmodel: MultivariateOUModel.java (+5 -105), PositiveDefiniteSubstitutionModel.java (+2 -39)
dong.w.xie 2010-03-03 08:46 Rev.: 3012

Trunk refactoring: finish MSSD (split parsers).

3 lines of code changed in 2 files:

  • src/dr/evomodel/substmodel: MutationDeathModel.java (new)
dong.w.xie 2010-02-17 16:12 Rev.: 2936

Trunk refactoring: make evoxml parsers more organized.

2 lines of code changed in 2 files:

  • src/dr/evomodel/substmodel: GLMSubstitutionModel.java (+2 -5)
dong.w.xie 2010-02-17 16:04 Rev.: 2935

Trunk refactoring: make subst parsers more organized.

14 lines of code changed in 18 files:

  • src/dr/evomodel/substmodel: BinaryCovarionModel.java (+1 -1), CovarionGTR.java (+1 -1), CovarionHKY.java (new), FrequencyModel.java (new), GTR.java (new), GeneralSubstitutionModel.java (+1 -1), SVSGeneralSubstitutionModel.java (+2 -2), TN93.java (+1 -1), TwoStateCovarionModel.java (+1 -2), YangCodonModel.java (new)
dong.w.xie 2010-02-17 14:56 Rev.: 2931

Trunk refactoring: complex substitution model (split parsers).

0 lines of code changed in 2 files:

  • src/dr/evomodel/substmodel: ComplexSubstitutionModel.java (-145), GLMSubstitutionModel.java (-62)
dong.w.xie 2010-02-17 12:29 Rev.: 2930

Trunk refactoring: finish substitution model (split parsers).

7 lines of code changed in 4 files:

  • src/dr/evomodel/substmodel: EmpiricalAminoAcidModel.java (new), GTR.java (+2 -115), YangCodonModel.java (+3 -104)
dong.w.xie 2010-02-17 12:00 Rev.: 2929

Trunk refactoring: big part of substitution model (split parsers).

20 lines of code changed in 5 files:

  • src/dr/evomodel/substmodel: FrequencyModel.java (+4 -123), GeneralSubstitutionModel.java (+4 -100), SVSGeneralSubstitutionModel.java (+5 -4), SubstitutionEpochModel.java (+1 -63), TN93.java (+6 -59)
dong.w.xie 2010-02-17 10:25 Rev.: 2927

Trunk refactoring: substitution model - binary (spilt parsers).

12 lines of code changed in 8 files:

  • src/dr/evomodel/substmodel: AbstractCovarionModel.java (new), AbstractSubstitutionModel.java (new), BinaryCovarionModel.java (+2 -80), CovarionGTR.java (+2 -97), CovarionHKY.java (+3 -72), TwoStateCovarionModel.java (+2 -76)
msuchard 2009-11-19 08:30 Rev.: 2553

Standardizing output between different CSM implementations

23 lines of code changed in 1 file:

  • src/dr/evomodel/substmodel: ComplexSubstitutionModel.java (+23 -7)
alexei.drummond 2009-11-10 11:42 Rev.: 2525

small code changes for binary covarion model

5 lines of code changed in 1 file:

  • src/dr/evomodel/substmodel: BinaryCovarionModel.java (+5 -9)

(146 more)

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