StatSVN - Directory src/dr/app/beagle/evomodel/sitemodel/

Author	Changes	Lines of Code	Lines per Change
Totals	97 (100.0%)	4630 (100.0%)	47.7
fbielejec	49 (50.5%)	2805 (60.6%)	57.2
msuchard	26 (26.8%)	1312 (28.3%)	50.4
rambaut	22 (22.7%)	513 (11.1%)	23.3

Most Recent Commits

rambaut 2012-11-15 14:45 Rev.: 5230

Updated copyright messages.

8 lines of code changed in 12 files:

src/dr/app/beagle/evomodel/sitemodel: BranchSubstitutionModel.java (new), EpochBranchSubstitutionModel.java (new), ExternalInternalBranchSubstitutionModel.java (+1 -1), GammaSiteRateModel.java (new), HomogenousBranchSubstitutionModel.java (new), SiteRateModel.java (new)

rambaut 2012-11-15 14:41 Rev.: 5229

Branch specific substitution models now working. NewTreeLikelihood will replace BeagleTreeLikelihood in a future commit. AncestralStateTL and MarkovJumpsTL now descend from NewTreeLikelihood. EpochBranchModel uses a different XML format from EpochBranchSubstitutionModel (now depreciated). Also implemented a branch-specific substitution model.

8 lines of code changed in 4 files:

src/dr/app/beagle/evomodel/sitemodel: BranchSubstitutionModel.java (+2), EpochBranchSubstitutionModel.java (+2), ExternalInternalBranchSubstitutionModel.java (+2), HomogenousBranchSubstitutionModel.java (+2)

fbielejec 2012-09-11 19:41 Rev.: 5151

cleaning code

36 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+36 -28)

fbielejec 2012-06-11 23:21 Rev.: 5031

safeguard from a null pointer exception if branch rate model is not specified

4 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+4 -1)

fbielejec 2012-06-08 23:33 Rev.: 5029

branch rate issues

41 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+41 -7)

fbielejec 2012-06-07 04:57 Rev.: 5021

code cleanup

12 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+12 -9)

fbielejec 2012-06-07 03:38 Rev.: 5020

make debugging easier

139 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+139 -108)

fbielejec 2012-05-23 22:13 Rev.: 4996

working on epoch ancestral state reco

26 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+26 -14)

fbielejec 2012-03-31 02:56 Rev.: 4911

cleaning the code

54 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+54 -68)

fbielejec 2012-03-31 02:25 Rev.: 4909

hide the debugging messages

14 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+14 -14)

fbielejec 2012-03-31 02:12 Rev.: 4908

only do the neccessary operations

23 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+23 -11)

fbielejec 2012-03-30 08:26 Rev.: 4906

sequential routine

46 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+46 -25)

fbielejec 2012-03-30 01:00 Rev.: 4905

...has been discontinued

3 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+3 -22)

fbielejec 2012-03-30 00:52 Rev.: 4904

Due to a shortage of devoted followers, the production of great leaders

37 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+37 -70)

fbielejec 2012-03-29 23:10 Rev.: 4903

Howe's Law: Everyone has a scheme that will not work

55 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+55 -15)

fbielejec 2012-03-29 08:50 Rev.: 4902

almost there

27 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+27 -32)

fbielejec 2012-03-29 01:49 Rev.: 4901

not to be used just yet

105 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+105 -30)

msuchard 2012-03-27 10:28 Rev.: 4896

Pinpointing Filip's bug

18 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+18 -2)

msuchard 2012-03-27 06:41 Rev.: 4894

Improved ability to co-opt an existing root height in StarTreeModel

353 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+353 -357)

fbielejec 2012-03-26 05:18 Rev.: 4887

cleaning the code

1 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+1 -1)

fbielejec 2012-03-26 04:55 Rev.: 4886

cleaning the code

6 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+6 -99)

msuchard 2012-03-25 09:24 Rev.: 4885

Fixed store/restore error in BeagleTreeLikelihood

29 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: HomogenousBranchSubstitutionModel.java (+29 -33)

fbielejec 2012-03-21 01:08 Rev.: 4878

reverting

107 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+107 -91)

fbielejec 2012-03-19 07:46 Rev.: 4866

I always forget

1 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+1 -1)

fbielejec 2012-03-19 06:02 Rev.: 4865

non-beagle implementation

96 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+96 -11)

fbielejec 2012-03-05 00:57 Rev.: 4763

lets keep it hidden

1 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+1 -1)

fbielejec 2012-03-05 00:51 Rev.: 4762

commiting everything

36 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+36 -46)

fbielejec 2012-02-18 03:32 Rev.: 4706

one boolean

2 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+2 -11)

fbielejec 2012-02-15 08:08 Rev.: 4693

dont print

10 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: HomogenousBranchSubstitutionModel.java (+10 -10)

fbielejec 2012-02-15 05:58

loop over the tree to determine the count

58 lines of code changed in 2 files:

src/dr/app/beagle/evomodel/sitemodel: BranchSubstitutionModel.java (+2 -1), EpochBranchSubstitutionModel.java (+56 -20)

fbielejec 2012-02-15 05:57

pass the tree as argument

20 lines of code changed in 2 files:

src/dr/app/beagle/evomodel/sitemodel: ExternalInternalBranchSubstitutionModel.java (+2 -1), HomogenousBranchSubstitutionModel.java (+18 -1)

fbielejec 2012-02-14 00:00 Rev.: 4681

memory efficiency

340 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+340 -299)

fbielejec 2012-02-05 10:46 Rev.: 4640

high speed low drag paralell convolution code that will strike fear into the hearts of our enemies - redux

3 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+3 -3)

fbielejec 2012-02-05 07:43 Rev.: 4639

high speed low drag paralell convolution code that will strike fear into the hearts of our enemies

121 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+121 -232)

fbielejec 2012-02-02 03:27 Rev.: 4626

reverting

0 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (-16)

fbielejec 2012-02-01 22:54 Rev.: 4624

CPU implementation

0 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (-6)

fbielejec 2012-02-01 22:33 Rev.: 4623

added the completely sequential equivalent

13 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+13 -5)

fbielejec 2012-02-01 21:55 Rev.: 4622

fixed a bug

1 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+1 -1)

fbielejec 2012-02-01 20:41 Rev.: 4621

working on routine populating transition matrices for many eigen buffers

58 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+58 -47)

fbielejec 2012-01-31 22:54 Rev.: 4619

imma spaghetti coder

235 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+235 -145)

(22 more)

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