StatSVN - Directory src/dr/evomodel/beagle/sitemodel/

Lines of Code

src/dr/evomodel/beagle/sitemodel/ Lines of Code

Developers

Author	Changes	Lines of Code	Lines per Change
Totals	16 (100.0%)	517 (100.0%)	32.3
rambaut	12 (75.0%)	501 (96.9%)	41.7
alexei.drummond	4 (25.0%)	16 (3.1%)	4.0

Most Recent Commits

rambaut 2009-08-04 03:47 Rev.: 2009

Moving BEAGLE/BEAST out of the main package into dr.app. This will allow us to deploy the jar file separately from BEAST.

0 lines of code changed in 4 files:

src/dr/evomodel/beagle/sitemodel: BranchSiteModel.java (del), GammaSiteRateModel.java (del), HomogenousBranchSiteModel.java (del), SiteRateModel.java (del)

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...

16 lines of code changed in 4 files:

src/dr/evomodel/beagle/sitemodel: GammaSiteRateModel.java (new), HomogenousBranchSiteModel.java (new)

rambaut 2009-03-19 05:23 Rev.: 1502

Towards a working beagle library

42 lines of code changed in 4 files:

src/dr/evomodel/beagle/sitemodel: BranchSiteModel.java (new), GammaSiteRateModel.java (+17), HomogenousBranchSiteModel.java (+23 -1)

rambaut 2009-03-19 02:15 Rev.: 1501

I have moved all the new stuff for the 'BEAGLE' library into its own package. I am producing a set of parsers that override the default ones to use the new classes. I envisage that at some point we will want to move to the new SubstModel hierarchy as it is much cleaner. But to avoid breaking anything whilst this develops, I am compartmentalizing them.

459 lines of code changed in 4 files:

src/dr/evomodel/beagle/sitemodel: BranchSiteModel.java (+15), GammaSiteRateModel.java (+328), HomogenousBranchSiteModel.java (+40), SiteRateModel.java (new 76)