Lines of Code
[root]/src/dr/app/beagle/evomodel/substmodel
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 241 (100.0%) | 8418 (100.0%) | 34.9 |
| rambaut | 105 (43.6%) | 4415 (52.4%) | 42.0 |
| msuchard | 131 (54.4%) | 3940 (46.8%) | 30.0 |
| jheled | 4 (1.7%) | 62 (0.7%) | 15.5 |
| fbielejec | 1 (0.4%) | 1 (0.0%) | 1.0 |
Reconstructions from AncestralStateBeagleTreeLikelihood now follow useAmbiguities=true/false setting.
17 lines of code changed in 2 files:
Standardizing output for markov jumps
7 lines of code changed in 2 files:
Improving ease to subclass ComplexSubstitutionModel for varying conditioning restrictions
27 lines of code changed in 4 files:
Increased max iterations and largest allowable condition number for complex diagonalizable substitution models; may change inference in BSSVS models.
6 lines of code changed in 1 file:
Standardizing format for complete histories with single events
4 lines of code changed in 2 files:
Modified NexusImporter to handle nested arrays. May cause unforeseen bugs in important other traits.
10 lines of code changed in 1 file:
Consistently clearing complete histories within CodonPartitionedRobustCounting
33 lines of code changed in 1 file:
Removed the canReturnComplexDiagonalization() method which was always returning false even if there was a complex diagonalization. This method is correctly returned by the substitution model.
0 lines of code changed in 2 files:
Incomplete implementation of multi-state stochastic Dollo under BEAGLE. Needs considerably more work.
176 lines of code changed in 1 file:
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 2 files:
Updated copyright messages.
529 lines of code changed in 62 files:
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.
2 lines of code changed in 2 files:
Porting 'evaluateLate' interface method from 1.7 branch.
16 lines of code changed in 2 files:
Porting fixes from 1.7.3 back into the trunk
26 lines of code changed in 2 files:
fixed typo
1 lines of code changed in 1 file:
Standardizing format for change events; these should always be an array of arrays because the number of events is variable.
2 lines of code changed in 1 file:
Logging of complete histories to trees has a more consistent format (a set of nested arrays).
14 lines of code changed in 1 file:
Improving complete history loggin format.
21 lines of code changed in 1 file:
ProductChainSubstitutionModel now propogates submodel changes
20 lines of code changed in 2 files:
Fixing reporting of site- and branch-specific S and N counts
22 lines of code changed in 3 files:
Added a trait logger for complete histories with times under robust dnds counting
31 lines of code changed in 1 file:
Expanding robust counting dNdS to consider complete histories
80 lines of code changed in 2 files:
Implemented TN93 under BEAGLE.
152 lines of code changed in 1 file:
Bug fix in randomization for SVSComplexSubstitutionModel
1 lines of code changed in 1 file:
Fixed a few more '!' in user interface messages. Let's keep them for errors that shouldn't happen (i.e., are genuine surprises).
1 lines of code changed in 1 file:
Improved user-friendliness of robust counting errors
15 lines of code changed in 1 file:
uncommitting an erroneous revision
0 lines of code changed in 6 files:
Adding TreeAnnonator parsing ability for MarkovJumps processes with multiple sites. To be used in Markov-modulated substitution models with Chris Simon.
1 lines of code changed in 1 file:
Playing with complete history logging; honeymoons are meant for bug-fixing
15 lines of code changed in 1 file:
Stationary distribution of Markov-modulated process now factors into the root frequency distribution of the sequence likelihood
156 lines of code changed in 3 files:
Intermediate work on a Markov-modulated mixture model; returns equal (and correct) sequence likelihoods when mixing rates = 0.
148 lines of code changed in 2 files:
Fixed incorrect calculations when using a BranchSubstitutionModel with MarkovJumps
2 lines of code changed in 1 file:
Uniformized simulation now falls back on rejection sampling when numerically instable.
31 lines of code changed in 1 file:
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.
21 lines of code changed in 2 files:
Work on dependent evolution between pairs of amino acids
239 lines of code changed in 2 files:
Some new empirical codon models by Stefan Zoller (ETH Zurich) & Adrian Schneider (U. of Edinburgh). Example files in examples/release/EmpiricalCodonModels
1021 lines of code changed in 5 files:
Almost certainly broke BeagleTreeLikelihood. Added support for BranchSiteModel (different substitution models across various sets of branches) and implemented an external vs internal branch-specific substitution process.
3 lines of code changed in 1 file:
Updates to robust counting classes to provide branch-specific unconditioned counts
84 lines of code changed in 1 file:
These models now allow a null indicator parameter in the constructor in which case they create one full of ones.
16 lines of code changed in 2 files:
Special tolerance test for super-high precision Colt eigendecomposition
2 lines of code changed in 1 file:
(54 more)