Lines of Code
[root]/src/dr/evomodel/transmission
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 43 (100.0%) | 1874 (100.0%) | 43.5 |
| rambaut | 7 (16.3%) | 1219 (65.0%) | 174.1 |
| alexei.drummond | 10 (23.3%) | 339 (18.1%) | 33.9 |
| msuchard | 7 (16.3%) | 255 (13.6%) | 36.4 |
| jheled | 13 (30.2%) | 57 (3.0%) | 4.3 |
| philippe.lemey@gmail.com | 3 (7.0%) | 2 (0.1%) | 0.6 |
| dong.w.xie | 3 (7.0%) | 2 (0.1%) | 0.6 |
Transmission statistic now updates the transmission history and accomodates estimated transmission times
1 lines of code changed in 2 files:
text message changes for the renaissance counting method in AncestralStatesOptionsPanel
1 lines of code changed in 1 file:
Tweaks to hierarchical transmission model
4 lines of code changed in 2 files:
Implementing a hierarchical version of the transmission model
251 lines of code changed in 5 files:
Trunk refactoring: make evoxml parsers more organized.
2 lines of code changed in 3 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...
10 lines of code changed in 3 files:
Beginning of refactoring to remove dr.inference.* dependency on dr.xml. Will take a while...
173 lines of code changed in 2 files:
Continued Marc's refactorization. I wonder what other shared functionality we can pull off in there.
0 lines of code changed in 1 file:
add a nethod for getting a meaningfull name of a likelihood. more classes may benefit from overriding the default.
18 lines of code changed in 1 file:
Moved ParameterChangeType -> Parameter.ChangeType
6 lines of code changed in 2 files:
added variable size functionality to Parameter
102 lines of code changed in 2 files:
Code Police
2 lines of code changed in 1 file:
A few tweaks.
354 lines of code changed in 1 file:
Change method name to something I understand
5 lines of code changed in 1 file:
Move getParameter and replaceParameter to AbstractXMLObjectParser - now used by multiple parsers
Renamed getSocketChild
Added generic 'public <T> T getAttribute(String name, T defaultValue)' to XMLObject - some usages of getXXXXattribute replaced. Update usage in your code if possible so we can one day remove the numerous getXXXXattribute
18 lines of code changed in 6 files:
Added Graham Jones' comments on Yule model prior
48 lines of code changed in 1 file:
Transmission history stuff progressing...
56 lines of code changed in 2 files:
Removed vestigal 'adoptState' methods that had been proliferating like endogenous retroviruses dispite that the method had been removed from the interface.
0 lines of code changed in 1 file:
change units type to an enum
Allow a log file name to be relative to main beast xml file when prefixed with a ./
minor jdoc and 1.5 cleanup
14 lines of code changed in 3 files:
Merged some more fixes and improvements I made in the 1.4 branch in to the trunk. Mostly changes to the TransmissionHistory classes. An update to AdvancedTreeLikelihood (I think only Beth uses this). XMLDocumentationHandler can handle integers now. TreeLogger can log TreeColourings more generically.
809 lines of code changed in 3 files: