| Directory | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 84 (100.0%) | 3725 (100.0%) | 44.3 |
| src/dr/inference/operators/ | 19 (22.6%) | 1705 (45.8%) | 89.7 |
| src/dr/inference/trace/ | 18 (21.4%) | 435 (11.7%) | 24.1 |
| src/dr/math/distributions/ | 4 (4.8%) | 406 (10.9%) | 101.5 |
| src/dr/evomodel/substmodel/ | 3 (3.6%) | 330 (8.9%) | 110.0 |
| src/dr/inferencexml/distribution/ | 1 (1.2%) | 194 (5.2%) | 194.0 |
| src/dr/inferencexml/trace/ | 1 (1.2%) | 133 (3.6%) | 133.0 |
| src/dr/inference/mcmc/ | 13 (15.5%) | 131 (3.5%) | 10.0 |
| src/dr/inference/model/ | 3 (3.6%) | 95 (2.6%) | 31.6 |
| src/dr/app/beagle/tools/ | 3 (3.6%) | 86 (2.3%) | 28.6 |
| src/dr/evomodel/tree/ | 2 (2.4%) | 82 (2.2%) | 41.0 |
| src/dr/app/tools/ | 4 (4.8%) | 78 (2.1%) | 19.5 |
| examples/release/ | 2 (2.4%) | 37 (1.0%) | 18.5 |
| src/dr/app/beast/ | 3 (3.6%) | 4 (0.1%) | 1.3 |
| src/test/dr/app/beauti/ | 2 (2.4%) | 3 (0.1%) | 1.5 |
| src/dr/evomodelxml/substmodel/ | 2 (2.4%) | 2 (0.1%) | 1.0 |
| src/dr/app/gui/chart/ | 2 (2.4%) | 2 (0.1%) | 1.0 |
| src/dr/app/beagle/evomodel/parsers/ | 2 (2.4%) | 2 (0.1%) | 1.0 |
Reverted to how the parameters were set previously, the likelihoods were not being updated correctly.
26 lines of code changed in 1 file:
Fixed the MH ratio for the independent coalescent sampler.
16 lines of code changed in 2 files:
Then LG model can also be used in the ancestral sequence annotator.
7 lines of code changed in 2 files:
Added LG model to the test package.
3 lines of code changed in 2 files:
Allow the BEAGLE parser to use the LG amino acid model.
2 lines of code changed in 2 files:
Allow the BEAST parser to use the LG amino acid model.
2 lines of code changed in 2 files:
Added LG model to the available types.
1 lines of code changed in 2 files:
Added the LG model of amino acid evolution (Le and Gascuel, 2008).
329 lines of code changed in 1 file:
Allows for an independent coalescent to be drawn given a list of taxa and a demographic model. The generated tree is then copied into the existing treeModel.
171 lines of code changed in 1 file:
New version of an additional method to copy a proposed tree into the current treeModel.
19 lines of code changed in 1 file:
Bug fix when using prior sampling to estimate (log) marginal likelihoods.
3 lines of code changed in 2 files:
First version of an additional method to copy a proposed tree (for example, from the coalescentSimulator) into the current treeModel. At the moment, copying rates and traits is not yet implemented. These may need to be copied during a separate tree traversal, if the direct access to leftChild and rightChild cannot be circumvented ...
63 lines of code changed in 1 file:
Added transformations to the syntax rules of the adaptable variance MVN operator.
5 lines of code changed in 1 file:
More flexible version of the adaptable variance MVN operator with respect to the transformations, which can now be provided using XML specification.
160 lines of code changed in 1 file:
New version of the adaptable variance MVN operator. Transformation to the log scale is currently always performed, the Jacobian has been taken into account for the MH-ratio.
59 lines of code changed in 1 file:
Remove old version of the operator.
0 lines of code changed in 1 file:
Refactoring.
396 lines of code changed in 1 file:
Added option to specify the number of iterations using the initial covariance.
66 lines of code changed in 1 file:
Fixed citation error.
1 lines of code changed in 2 files:
Fixed typo.
1 lines of code changed in 2 files:
(46 more)