StatSVN - Directory src/dr/evomodel/arg/likelihood/

Lines of Code

src/dr/evomodel/arg/likelihood/ Lines of Code

Developers

Author	Changes	Lines of Code	Lines per Change
Totals	18 (100.0%)	1373 (100.0%)	76.2
msuchard	9 (50.0%)	1116 (81.3%)	124.0
alexei.drummond	4 (22.2%)	247 (18.0%)	61.7
bloomquist	1 (5.6%)	5 (0.4%)	5.0
jheled	3 (16.7%)	3 (0.2%)	1.0
rambaut	1 (5.6%)	2 (0.1%)	2.0

Most Recent Commits

msuchard 2010-11-12 02:11 Rev.: 3708

Temporary patch for bug in ARG model in which negative branch lengths arise.

18 lines of code changed in 2 files:

src/dr/evomodel/arg/likelihood: ARGLikelihood.java (new)

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...

2 lines of code changed in 2 files:

src/dr/evomodel/arg/likelihood: AbstractARGLikelihood.java (+2 -5)

jheled 2009-06-23 07:20 Rev.: 1794

automatic idea changes, change type return type of getChild

1 lines of code changed in 1 file:

src/dr/evomodel/arg/likelihood: ARGLikelihood.java (+1 -1)

msuchard 2009-04-22 10:40 Rev.: 1617

ARGModel now fully supports caching partial likelihood calculations even as nodes are added and remove from tree. Support is not fully implemented in the operators yet.

87 lines of code changed in 2 files:

src/dr/evomodel/arg/likelihood: ARGLikelihood.java (+86 -33), AbstractARGLikelihood.java (+1 -13)

msuchard 2009-04-20 12:48 Rev.: 1608

Started overhaul of ARG model likelihood calculations to cache unaffected partials (it's about time I did this). All changes to the ARG model, except for topological changes, appear to be caching correctly; speed-up is about 30% (for a small example, suspect much more for larger problems). I need to think harder about how to handle topological changes -- a simple map from old ARGTree nodes to ARGModel to new ARGTree nodes should suffice.

114 lines of code changed in 2 files:

src/dr/evomodel/arg/likelihood: ARGLikelihood.java (+99 -111), AbstractARGLikelihood.java (+15 -2)

msuchard 2009-04-20 06:05 Rev.: 1605

Refactored LikelihoodColumn as protected class in AbstractModelLikelihood (thanks, Joseph ... this was a good idea); removed subclassing of getLogColumns in several AMLs to see if this break things. I do not suspect that it will and we can/should now remove subclassing getLogColumns and redefinition of LikelihoodColumn in most AMLs, saving hundreds of lines of code .. or shotting myself in the foot :-)

0 lines of code changed in 1 file:

src/dr/evomodel/arg/likelihood: AbstractARGLikelihood.java (-22)

jheled 2009-04-19 08:35 Rev.: 1598

add a nethod for getting a meaningfull name of a likelihood. more classes may benefit from overriding the default.

2 lines of code changed in 2 files:

src/dr/evomodel/arg/likelihood: ARGLikelihood.java (-1), AbstractARGLikelihood.java (+2 -5)

bloomquist 2009-03-07 11:46 Rev.: 1483

Not positive yet, but fairly sure have joint rate variation estimation and ARG inference working.

5 lines of code changed in 1 file:

src/dr/evomodel/arg/likelihood: ARGLikelihood.java (+5 -2)

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

Moved ParameterChangeType -> Parameter.ChangeType

5 lines of code changed in 1 file:

src/dr/evomodel/arg/likelihood: AbstractARGLikelihood.java (+5 -2)

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

added variable size functionality to Parameter

240 lines of code changed in 1 file:

src/dr/evomodel/arg/likelihood: AbstractARGLikelihood.java (+240 -243)

rambaut 2008-10-12 23:14 Rev.: 1230

Simplified the SiteModel interface so it is no longer a wrapper for a substitution model to get transition probability matrix.

2 lines of code changed in 1 file:

src/dr/evomodel/arg/likelihood: ARGLikelihood.java (+2 -2)

msuchard 2008-08-14 11:09 Rev.: 1126

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).

897 lines of code changed in 2 files:

src/dr/evomodel/arg/likelihood: ARGLikelihood.java (+560), AbstractARGLikelihood.java (+337)