Lines of Code
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 62 (100.0%) | 1248 (100.0%) | 20.1 |
| Michael.DefoinPLatel | 23 (37.1%) | 930 (74.5%) | 40.4 |
| alexei.drummond | 19 (30.6%) | 225 (18.0%) | 11.8 |
| Sibon.Li@gmail.com | 1 (1.6%) | 69 (5.5%) | 69.0 |
| jheled | 10 (16.1%) | 14 (1.1%) | 1.4 |
| rambaut | 5 (8.1%) | 5 (0.4%) | 1.0 |
| dong.w.xie | 4 (6.5%) | 5 (0.4%) | 1.2 |
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).
4 lines of code changed in 4 files:
Trunk refactoring: branch rate and clock rate model (split parsers).
5 lines of code changed in 4 files:
Changed input format of ACLikelihood to allow incorporating other distributions (logSpace="true"/"false" replaced with distribution="logNormal"/"normal"/"inverseGaussian"
69 lines of code changed in 1 file:
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...
12 lines of code changed in 4 files:
refactoring to remove illegal dependencies (dr.inference should not depend on dr.evo*.*) and tidying
1 lines of code changed in 1 file:
Converted Autocorrelated Relaxed clock models to use new TreeParameterModel so that they have a similar pattern to Uncorrelated Relaxed clock models in the XML. Neither model now uses the <nodeRates> facility in TreeModel. Hopefully I haven't slowed anything down -- the test XML file suggests it gets the right answers at least!!
42 lines of code changed in 1 file:
More of the same - string constants
2 lines of code changed in 1 file:
A small improvment in reducing usage of litteral string constants.
Each constant should be defined in one place and referenced elsewhere.
The best place I found is in the various parsers. This may be wrong but now moving it elsewhere is a simple matter.
4 lines of code changed in 3 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.
2 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
96 lines of code changed in 2 files:
I finalize the intergration of the autocorrelated relaxed clock into Beauti. The final user still needs to be clever and check the settings of the priors (maybe some warnings should be added). In addition, I setup a test file for the autocorrelated model. Finally, I released Ziheng Yang's UNcorrelated model for further comparison with Drummond et al 2006 paper (so far I haven't seen any difference between the discretized and continuous version).
120 lines of code changed in 7 files:
Completed the intergration of the Autocorrelated clock model into Beauti + improvement in the model itself. I am still not happy with the special operators, so they should not be used so far.
27 lines of code changed in 2 files:
I added three operators for better mixing of rates with the autocorrelated model of rate of evolution
193 lines of code changed in 6 files:
moved all distributions into their own sub-package in dr.math
6 lines of code changed in 4 files:
Be very afraid: I have tidied up double and string attribute parsing in various classes. Hopefully no logic was changed, and I avoided code that couldn't be understood in a brief moment.
2 lines of code changed in 1 file:
Tidied up boolean attribute parsing in various classes
1 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
6 lines of code changed in 4 files:
Some improvements for mixing with relaxed clock models
9 lines of code changed in 2 files:
Autocorrelated clock model of rate evolution (Yang and Rannala 2006). This should eventualy replace former RateChangeLikelihood and {ED,GD,LN}Likelihood
364 lines of code changed in 2 files:
Fix the RatechangeLikelihood to get the autocorrelated clock model working. Rates can be absolute or relative.
217 lines of code changed in 4 files:
Removed vestigal 'adoptState' methods that had been proliferating like endogenous retroviruses dispite that the method had been removed from the interface.
1 lines of code changed in 1 file:
fixing some of the errors caused by adding TreeAttributeProvider and NodeAttributeProvider...
59 lines of code changed in 3 files: