StatSVN - Directory src/dr/evomodel/ibd/

Lines of Code

src/dr/evomodel/ibd/ Lines of Code

Developers

Author	Changes	Lines of Code	Lines per Change
Totals	15 (100.0%)	698 (100.0%)	46.5
alexander.alekseyenko	3 (20.0%)	571 (81.8%)	190.3
rambaut	6 (40.0%)	78 (11.2%)	13.0
alexei.drummond	6 (40.0%)	49 (7.0%)	8.1

Most Recent Commits

rambaut 2010-06-07 23:07 Rev.: 3235

Simplified TreeTrait interface to remove explicit dimensionality. If multidimensional traits are required then it needs to use double[] as the type.

6 lines of code changed in 4 files:

src/dr/evomodel/ibd: AvgPosteriorIBDReporter.java (+3 -7), IBDReporter.java (new)

rambaut 2010-06-02 22:53 Rev.: 3215

TreeTraits commit number 2. This one is a bit more wide ranging with potential to break things. 1) BranchAttributeProvider and NodeAttributeProvider have been deleted and replaced with a combination of TreeTraits and TreeTraitProviders. Sources implement TreeTraitProvider to say that they can provide information about nodes and branches. A good example of a class which has been generalized is AncestralState (in evomodel.treelikelihood) - this now just takes a TreeTrait and logs the trait for a given MRCA (the trait can be anything at all - whereas previously it took an AncestralStateTreeLikelihood).

72 lines of code changed in 2 files:

src/dr/evomodel/ibd: AvgPosteriorIBDReporter.java (+33 -13), IBDReporter.java (+39 -7)

alexei.drummond 2009-07-19 14:30 Rev.: 1873

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...

35 lines of code changed in 2 files:

src/dr/evomodel/ibd: AvgPosteriorIBDReporter.java (+5 -8), IBDReporter.java (+30 -8)

alexei.drummond 2008-11-27 21:21 Rev.: 1340

Moved ParameterChangeType -> Parameter.ChangeType

10 lines of code changed in 2 files:

src/dr/evomodel/ibd: AvgPosteriorIBDReporter.java (+5 -2), IBDReporter.java (+5 -2)

alexei.drummond 2008-11-27 13:08 Rev.: 1337

added variable size functionality to Parameter

4 lines of code changed in 2 files:

src/dr/evomodel/ibd: AvgPosteriorIBDReporter.java (+2 -5), IBDReporter.java (+2 -5)

alexander.alekseyenko 2008-11-15 04:27 Rev.: 1303

Added expected identy by descent node reporter.
IBDReporter -- marginal expectation of number of tips identical by descent
AvgPosteriorIBDPeporter -- the same but conditional on sites and averaged over the alignment

571 lines of code changed in 3 files:

src/dr/evomodel/ibd: AvgPosteriorIBDReporter.java (+278), HKYRates.java (new 52), IBDReporter.java (+241)