| Directory | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 157 (100.0%) | 10501 (100.0%) | 66.8 |
| src/dr/evomodel/MSSD/ | 21 (13.4%) | 1522 (14.5%) | 72.4 |
| examples/ | 13 (8.3%) | 1196 (11.4%) | 92.0 |
| src/dr/evomodel/treelikelihood/ | 11 (7.0%) | 883 (8.4%) | 80.2 |
| src/dr/inference/prior/ | 5 (3.2%) | 800 (7.6%) | 160.0 |
| src/dr/app/bfe/ | 8 (5.1%) | 744 (7.1%) | 93.0 |
| src/dr/evomodel/ibd/ | 3 (1.9%) | 571 (5.4%) | 190.3 |
| src/dr/xml/ | 5 (3.2%) | 406 (3.9%) | 81.2 |
| src/dr/evomodel/approxPopTree/ | 5 (3.2%) | 405 (3.9%) | 81.0 |
| src/dr/inference/model/ | 4 (2.5%) | 386 (3.7%) | 96.5 |
| src/dr/app/beast/ | 13 (8.3%) | 378 (3.6%) | 29.0 |
| src/dr/evolution/datatype/ | 4 (2.5%) | 371 (3.5%) | 92.7 |
| src/dr/inference/operators/ | 5 (3.2%) | 370 (3.5%) | 74.0 |
| src/dr/inference/mcmc/ | 8 (5.1%) | 341 (3.2%) | 42.6 |
| src/dr/math/distributions/ | 3 (1.9%) | 335 (3.2%) | 111.6 |
| src/dr/evomodel/substmodel/ | 4 (2.5%) | 308 (2.9%) | 77.0 |
| examples/release/ | 4 (2.5%) | 235 (2.2%) | 58.7 |
| src/dr/evoxml/ | 3 (1.9%) | 225 (2.1%) | 75.0 |
| src/dr/evomodelxml/ | 3 (1.9%) | 217 (2.1%) | 72.3 |
| examples/unrelease/ | 7 (4.5%) | 214 (2.0%) | 30.5 |
| src/dr/evolution/alignment/ | 3 (1.9%) | 161 (1.5%) | 53.6 |
| src/dr/evomodel/branchratemodel/ | 2 (1.3%) | 153 (1.5%) | 76.5 |
| src/dr/util/ | 3 (1.9%) | 119 (1.1%) | 39.6 |
| src/dr/inferencexml/operators/ | 3 (1.9%) | 85 (0.8%) | 28.3 |
| src/dr/inference/trace/ | 2 (1.3%) | 33 (0.3%) | 16.5 |
| src/dr/math/ | 3 (1.9%) | 14 (0.1%) | 4.6 |
| src/dr/evomodel/tree/ | 2 (1.3%) | 11 (0.1%) | 5.5 |
| src/dr/app/beagle/evomodel/parsers/ | 1 (0.6%) | 8 (0.1%) | 8.0 |
| src/dr/evomodelxml/substmodel/ | 1 (0.6%) | 6 (0.1%) | 6.0 |
| src/dr/evolution/tree/ | 1 (0.6%) | 4 (0.0%) | 4.0 |
| src/dr/evomodel/alternativesplicing/ | 4 (2.5%) | 0 (0.0%) | 0.0 |
| examples/incorrect/ | 3 (1.9%) | 0 (0.0%) | 0.0 |
resolving Issue 630.
3 lines of code changed in 1 file:
renamed integratedMixtureModel to MixtureModelLikelihood. Preserved an alias parser <integratedMixtureModel> per Marc's request. Updated the class, such that the mixtures are always normalized internally when likelihood is calculated.
254 lines of code changed in 7 files:
Started on a model to compute mixtures of likelihoods.
147 lines of code changed in 3 files:
Updated Compound DirichletMultinomial distribution to use both the rates and frequencies + dispersion parametrization. New example XML included.
176 lines of code changed in 3 files:
Started MV Polya Likelihood model
343 lines of code changed in 6 files:
fix and move a few example files of my making
249 lines of code changed in 10 files:
add a new operator on sum constrained parameter, providing better mixing for multiscale parameters
216 lines of code changed in 3 files:
Fixed a small bug that prevented beagle from using multiple instances when certain patterns are used.
30 lines of code changed in 1 file:
Started on Population Tree Approximation models.
459 lines of code changed in 9 files:
Fixed burn-in issues in MLE, restructured integration procedure, now using Integrator classes for handling different integration schemes.
146 lines of code changed in 2 files:
Minor changes to Path Sampling Marginal Likelihood Estimation and Bayes Factor analysis, including:
- Operator analysis printer class (general purpose);
- Operator schedule, critical bug fix;
- Path likelihood clean-up;
- Marginal likelihood estimator minor behavior changes.
202 lines of code changed in 6 files:
making path sampling work for computing Bayes Factors; changes:
- new class that can combine MCMC operator schedules
- marginalLikelihoodEstimator can take multiple mcmc objects now
- changed format of PathSamplingAnalysis output (e.g. can copy-paste the pathParameter vs. meanPathLikelihood into a plotting program for evaluation and integration)
133 lines of code changed in 3 files:
added parsers for Lewis' Mk model with totaly ordered/unordered/custom ordered states.
307 lines of code changed in 7 files:
making stochastic Dollo compliant with the new DataType stuff...
7 lines of code changed in 1 file:
adding the files missing from r1812
359 lines of code changed in 3 files:
Started a GUI for Bayes Factor Analysis of BEAST generated xml model.
744 lines of code changed in 8 files:
minor adjustments to path sampling code
1) user can specify the amount of burn-in through a corresponding attribute
2) the pathParameter column is now labeled as such; this was done by fixing how properties get logged
172 lines of code changed in 6 files:
added an example of binary stochastic Dollo model, +some minor related bug fixes.
268 lines of code changed in 3 files:
Added implementation of Lewis' Mk Model (cf. Syst. Biol. 50(6):913-925, 2001)
65 lines of code changed in 2 files:
Massive refactoring of MSSD model specification. See new example file testMSSD.xml to appreciate the resulting simplifications.
377 lines of code changed in 7 files:
(13 more)