Lines of Code
[root]/src/dr/evomodel/arg/branchratemodel
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 6 (100.0%) | 477 (100.0%) | 79.5 |
| msuchard | 1 (16.7%) | 307 (64.4%) | 307.0 |
| alexei.drummond | 3 (50.0%) | 168 (35.2%) | 56.0 |
| rambaut | 2 (33.3%) | 2 (0.4%) | 1.0 |
This update does a number of things. 1) TreeLoggerParser and DemographicLoggerParser were in dr.inferencexml which breaks the dependency rules as they link to things in dr.evomodel. These are now moved to dr.evomodelxml. 2) A dr.evolution.tree.TreeTrait interface is created which is a general purpose interface for access to traits on nodes/branches. BranchAttributeProvider and NodeAttributeProvider will be replaced by this interface in the next update. 3) All BranchRateModels now have a common abstract base class AbstractBranchRateModel to implement their common features (these now implement TreeTrait to provide rates).
2 lines of code changed in 2 files:
Parameter -> Variable, Act 2 -- this is probably the biggest change made to core BEAST in a few years. So I tagged revision 1870 for convenience. Parameter is now basically obsoleted and should be replaced by DoubleVariable or Variable<Double> where appropriate. We can now also develop some Variable<Integer> and Variable<Boolean> et cetera so should be nice in the future... I have also added a Variable<double[]> for vectors and matrices. See dr.inference.tutorial.Tutorial1 for a first peek at programmable BEAST MCMC...
8 lines of code changed in 1 file:
Moved ParameterChangeType -> Parameter.ChangeType
1 lines of code changed in 1 file:
added variable size functionality to Parameter
159 lines of code changed in 1 file:
Port of ARG classes into the trunk. There are some very silly repeats of code (namely: TreeModel and ARGModel should inherit from a base class, ARGTreeLogger is almost indentical to TreeLogger, and CompoundParameter should replace ARGCompoundParameter).
307 lines of code changed in 1 file: