Lines of Code
[root]/src/dr/evomodel/coalescent/operators
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 97 (100.0%) | 9400 (100.0%) | 96.9 |
| julia.pal.r@gmail.com | 27 (27.8%) | 3852 (41.0%) | 142.6 |
| msuchard | 15 (15.5%) | 1835 (19.5%) | 122.3 |
| bloomquist | 14 (14.4%) | 1236 (13.1%) | 88.2 |
| mandevsgill | 6 (6.2%) | 805 (8.6%) | 134.1 |
| gerton.lunter | 5 (5.2%) | 763 (8.1%) | 152.6 |
| alexei.drummond | 11 (11.3%) | 737 (7.8%) | 67.0 |
| jheled | 9 (9.3%) | 161 (1.7%) | 17.8 |
| dong.w.xie | 8 (8.2%) | 7 (0.1%) | 0.8 |
| rambaut | 2 (2.1%) | 4 (0.0%) | 2.0 |
Latest version with new operator for joint--TODO: let Parameters.restore for vectors with different sizes. Tracer analysis doesn't read log files with {num,num,..}
938 lines of code changed in 3 files:
adding elements to store-restore
2 lines of code changed in 1 file:
small change
3 lines of code changed in 1 file:
working on summary - need to calculate "sigmoidal" medians, etc
59 lines of code changed in 1 file:
added the "tracer" analysis similar to EBSP
1 lines of code changed in 1 file:
Special logger
28 lines of code changed in 1 file:
works -fixed Slice sampling detail
126 lines of code changed in 1 file:
a working version for fixed genealogy
19 lines of code changed in 1 file:
like GibbsOperator --not the right thing to do but temporal solution
58 lines of code changed in 1 file:
updating
13 lines of code changed in 1 file:
just updating - need to see why infty in SliceSampler. It fails in Oldscore vs currentScore
47 lines of code changed in 1 file:
Parameterizing a lot and changes in number of latents, location of latents..need to fix GP sampling of one point, problem with "last" neighbor
232 lines of code changed in 1 file:
fixed coalescent interval in Likelihood suff. stat and small testing to Block Update
28 lines of code changed in 1 file:
testing GPBlockUpdate -trying to understand Prior value
333 lines of code changed in 1 file:
Not finished but descent version of GPOperator - fixing imports :S
0 lines of code changed in 1 file:
Not finished but descent version of GPOperator
117 lines of code changed in 1 file:
still working on GPOperator
472 lines of code changed in 1 file:
Not finished but descent version of GPOperator
506 lines of code changed in 1 file:
Updating Likelihood, need to add the GMRF part
24 lines of code changed in 1 file:
updating small changes in operators and adding lambda_parameter
29 lines of code changed in 1 file:
updating small changes in operators and adding lambda_parameter
17 lines of code changed in 1 file:
Editing mainly GPSLikelihoodParser
4 lines of code changed in 1 file:
Creating evomodelxml..GaussianProcessSkytrackBlockUpdateOperator and renamed GPSkytrackBlockUpdateIperator from evomodel..
398 lines of code changed in 2 files:
Editing GaussianProcessSkytrackLikelihood.java and creating operators
398 lines of code changed in 1 file:
Now the multilocus Skyride model should work.
0 lines of code changed in 2 files:
Multilocus GMRF model has been updated and appears to be working properly. Old GMRF model should still work with the old xml syntax.
377 lines of code changed in 2 files:
Cleaned-up version of GMRFMultilocusSkyrideLikelihood. It appears to be working with the block update sampler.
6 lines of code changed in 1 file:
GMRF multilocus likelihood appears to compute properly; operators still do not work and there is debugging material to remove.
422 lines of code changed in 1 file:
Trunk refactoring: finish GMRF (split parsers).
5 lines of code changed in 4 files:
Trunk refactoring: 2nd part of coalescent (split parsers).
2 lines of code changed in 4 files:
Added a very simple path sampling example and some minor tweaks to GMRF skyrides and the TraitGibbsOperator
3 lines of code changed in 1 file:
Do not terminate run if distribution quantile is not up to scratch. Just let the operator fail.
7 lines of code changed in 1 file:
more automatic intelliJ
7 lines of code changed in 1 file:
moved all distributions into their own sub-package in dr.math
6 lines of code changed in 2 files:
renamed mispelled method (setSumDeviation), added CoercionMode enum and refactored autoOptimize parsing accordingly. Added ability to log to memory and import newick from string.
5 lines of code changed in 1 file:
Be scared: I have tidied up integer attribute parsing in various classes. Also operator weights were integers in some places -- they should all be doubles now...
2 lines of code changed in 1 file:
Tidied up boolean attribute parsing in various classes
315 lines of code changed in 2 files:
fixed spelling :-0)
4 lines of code changed in 1 file:
Marc changes in the GMRFBlockUpdater require the scaleFactor to be greater than 1.0. Changed the error message in the parser to reflect this.
1 lines of code changed in 1 file:
Fixed annoying logging problem in GMRFSkyrideBlockUpdater.
1 lines of code changed in 1 file:
(32 more)