Directory src/dr/inference/markovjumps/

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msuchard 2012-12-18 06:51 Rev.: 5282

Consistently clearing complete histories within CodonPartitionedRobustCounting

8 lines of code changed in 2 files:

• src/dr/inference/markovjumps: StateHistory.java (new)

rambaut 2012-11-22 04:11 Rev.: 5252

Cleaned up the format of the complete history logging. Now has {{SITE,TIME,FROM_STATE,TO_STATE},...}. I am aware this will mess up people's processing scripts but it was a mess before (unnecessary nesting of parentheses and '-1's all over the place).

3 lines of code changed in 1 file:

• src/dr/inference/markovjumps: StateHistory.java (+3 -2)

rambaut 2012-11-22 01:29 Rev.: 5251

Cleaned up the format of the complete history logging. Now has {SITE,{TIME,FROM_STATE,TO_STATE},...}. I am aware this will mess up people's processing scripts but it was a mess before (unnecessary nesting of parentheses and '-1's all over the place).

8 lines of code changed in 1 file:

• src/dr/inference/markovjumps: StateHistory.java (+8 -7)

msuchard 2012-06-23 09:32 Rev.: 5043

Fixing inconsistency when reporting a filtered state-change history

56 lines of code changed in 3 files:

• src/dr/inference/markovjumps: StateChange.java (new), StateHistory.java (+10 -1)

msuchard 2012-06-23 08:34 Rev.: 5042

Standardizing format for change events; these should always be an array of arrays because the number of events is variable.

3 lines of code changed in 1 file:

• src/dr/inference/markovjumps: StateHistory.java (+3 -2)

msuchard 2012-06-23 03:20 Rev.: 5041

Possible new string format for change events

38 lines of code changed in 1 file:

• src/dr/inference/markovjumps: StateHistory.java (+38 -10)

rambaut 2012-06-07 00:48 Rev.: 5018

Logging of complete histories to trees has a more consistent format (a set of nested arrays).

3 lines of code changed in 1 file:

• src/dr/inference/markovjumps: StateHistory.java (+3 -3)

msuchard 2012-06-05 09:09 Rev.: 5012

Fixing reporting of site- and branch-specific S and N counts

20 lines of code changed in 1 file:

• src/dr/inference/markovjumps: StateHistory.java (+20)

msuchard 2011-09-29 04:58 Rev.: 4338

Improved user-friendliness of robust counting errors

2 lines of code changed in 2 files:

• src/dr/inference/markovjumps: SubordinatedProcess.java (new)

msuchard 2011-08-08 11:40 Rev.: 4165

Added flexibility to check numerical stability of BSSVS substitution models

11 lines of code changed in 1 file:

• src/dr/inference/markovjumps: SubordinatedProcess.java (+11 -4)

msuchard 2011-05-31 06:47 Rev.: 3993

Playing with complete history logging; honeymoons are meant for bug-fixing

47 lines of code changed in 2 files:

• src/dr/inference/markovjumps: StateChange.java (+3), StateHistory.java (+44 -3)

msuchard 2011-05-09 09:29 Rev.: 3972

Re-implemented logging of random local clock indicators in tree log files; this ability was lost when we converted over to tree traits.

1 lines of code changed in 1 file:

• src/dr/inference/markovjumps: SubordinatedProcess.java (+1 -1)

msuchard 2011-05-08 06:57 Rev.: 3971

Fixed incorrect calculations when using a BranchSubstitutionModel with MarkovJumps

2 lines of code changed in 1 file:

• src/dr/inference/markovjumps: SubordinatedProcess.java (+2 -2)

msuchard 2011-04-29 10:18 Rev.: 3968

Uniformized simulation now falls back on rejection sampling when numerically instable.

22 lines of code changed in 3 files:

• src/dr/inference/markovjumps: SubordinatedProcess.java (+20 -6), UniformizedStateHistory.java (new)

msuchard 2011-04-27 15:50 Rev.: 3962

Added logging ability for complete substitution history under uniformization; there is a high likelihood that I broke some of the Markov jumps/reward mechanisms in this update.

26 lines of code changed in 3 files:

• src/dr/inference/markovjumps: MarkovJumpsType.java (new), StateHistory.java (+25)

msuchard 2011-03-21 07:57 Rev.: 3885

Tracking down numerical instability for very long and very short simulation times under Hobolth's algorithm

11 lines of code changed in 1 file:

• src/dr/inference/markovjumps: SubordinatedProcess.java (+11 -8)

msuchard 2010-06-24 03:52 Rev.: 3281

Modifying CodonPartitionedRobustCounting to differentiate between internal and external branches; minor optimization of uniformized state history simulation

25 lines of code changed in 2 files:

• src/dr/inference/markovjumps: StateHistory.java (+12 -2), SubordinatedProcess.java (+13 -1)

msuchard 2010-06-15 09:39 Rev.: 3269

Fixed bug in rewards; JUnitTests are awesome

1 lines of code changed in 1 file:

• src/dr/inference/markovjumps: StateHistory.java (+1 -1)

msuchard 2010-06-15 08:26 Rev.: 3268

Fixed store/restore of subordinated process for Uniformization; also fixed reward process for Uniformization

34 lines of code changed in 2 files:

• src/dr/inference/markovjumps: StateHistory.java (+1 -1), SubordinatedProcess.java (+33 -1)

msuchard 2010-06-13 04:48 Rev.: 3258

Better immediate calculation caching for MarkovJumps

47 lines of code changed in 2 files:

• src/dr/inference/markovjumps: MarkovJumpsCore.java (new)

msuchard 2010-04-24 06:58 Rev.: 3132

MarkovJumpsBeagleTreeLikelihood now supports all CTMC that can be uniformized (I believe this is all finite-state models).

9 lines of code changed in 2 files:

• src/dr/inference/markovjumps: StateHistory.java (+5 -1), UniformizedStateHistory.java (+4 -4)

msuchard 2010-03-27 11:58 Rev.: 3079

Completed UnitTest for simulation via Uniformization; added UniformizedSubstitutionModel to connect MarkovJumpsTreeLikelihood with the Uniformization method

1 lines of code changed in 2 files:

• src/dr/inference/markovjumps: UniformizedMarkovJumpsCore.java (del), UniformizedStateHistory.java (+1 -5)

msuchard 2010-03-26 11:04 Rev.: 3074

Added methods to simulate end-conditioned CTMC using the Uniformization method; this is the most optimal, simulation algorithm available and should make Stochastic Mapping and Coalescent-with-Migration models much, much faster (when real eigen decompositions are not available ... if the model is real diagonalizable MarkovJumps is still the way to go)

341 lines of code changed in 4 files:

• src/dr/inference/markovjumps: MarkovJumpsCore.java (+4 -4), StateHistory.java (+15 -6), SubordinatedProcess.java (+211), UniformizedStateHistory.java (+111)

msuchard 2010-03-25 13:02 Rev.: 3071

Can now simulate (and report) the complete history of any model in BEAST, most importantly codon models (with branch rate variation) and report the true number of synonymous and nonsynonymous mutations in a synthetic dataset.

33 lines of code changed in 2 files:

• src/dr/inference/markovjumps: MarkovJumpsRegisterAcceptor.java (new 14), StateHistory.java (+19 -5)

msuchard 2010-03-25 06:23 Rev.: 3070

Further work for RobustCounting

220 lines of code changed in 2 files:

• src/dr/inference/markovjumps: StateChange.java (+60), StateHistory.java (+160)

msuchard 2010-03-12 11:40 Rev.: 3038

Trimming code from MarkovJumpCore

49 lines of code changed in 2 files:

• src/dr/inference/markovjumps: MarkovJumpsCore.java (+19 -41), UniformizedMarkovJumpsCore.java (new 30)

msuchard 2010-02-26 15:46 Rev.: 2988

Added JUnitTest for counting synonymous jumps; also refactored a function in making codon models to avoid duplicating code

0 lines of code changed in 1 file:

• src/dr/inference/markovjumps: CodonLabeling.java (del)

msuchard 2010-02-24 03:53 Rev.: 2965

Intermediate steps in implementing robust counting of S and N using nucleotide models

7 lines of code changed in 1 file:

• src/dr/inference/markovjumps: CodonLabeling.java (new 7)

msuchard 2010-02-24 03:52 Rev.: 2964

Refactoring MarkovJumpsCore after Asger Hobolth reminded me that one wants to compute more than just the mean process

34 lines of code changed in 2 files:

• src/dr/inference/markovjumps: MarkovJumpsCore.java (+3 -3), UniformizedMarkovJumpsCore.java (+31)

msuchard 2010-02-16 20:52 Rev.: 2926

(1) Small fix to trait rate Gibbs operator and (2) initial classes for robust counting on codon partitioned models

35 lines of code changed in 1 file:

• src/dr/inference/markovjumps: CodonLabeling.java (+35)

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.

44 lines of code changed in 2 files:

• src/dr/inference/markovjumps: MarkovJumpsCore.java (+8 -5), MarkovJumpsType.java (+36)

msuchard 2009-11-25 13:49 Rev.: 2597

Interfacing markovjumps to a TreeLikelihood for jump reconstruction

6 lines of code changed in 1 file:

• src/dr/inference/markovjumps: MarkovJumpsCore.java (+6 -2)

msuchard 2009-11-22 05:13 Rev.: 2577

Refactoring markovjumps into a core and a wrapper

233 lines of code changed in 1 file:

• src/dr/inference/markovjumps: MarkovJumpsCore.java (+233)