operators
(7 files, 501 lines)
structure
(4 files, 1009 lines)
[root]/src/dr/evomodel/coalescent
operators
(7 files, 501 lines)
structure
(4 files, 1009 lines)
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 483 (100.0%) | 22919 (100.0%) | 47.4 |
| alexei.drummond | 82 (17.0%) | 4697 (20.5%) | 57.2 |
| msuchard | 47 (9.7%) | 3784 (16.5%) | 80.5 |
| rambaut | 54 (11.2%) | 3719 (16.2%) | 68.8 |
| jheled | 126 (26.1%) | 3597 (15.7%) | 28.5 |
| bloomquist | 39 (8.1%) | 3477 (15.2%) | 89.1 |
| julia.pal.r@gmail.com | 33 (6.8%) | 1812 (7.9%) | 54.9 |
| mandevsgill | 14 (2.9%) | 1539 (6.7%) | 109.9 |
| dong.w.xie | 81 (16.8%) | 188 (0.8%) | 2.3 |
| gerton.lunter | 2 (0.4%) | 101 (0.4%) | 50.5 |
| vminin | 3 (0.6%) | 3 (0.0%) | 1.0 |
| jen.tom | 1 (0.2%) | 1 (0.0%) | 1.0 |
| fbielejec | 1 (0.2%) | 1 (0.0%) | 1.0 |
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,..}
129 lines of code changed in 4 files:
Reimplemented lazy evaluation in Skygrid and cleaned up formatting.
497 lines of code changed in 4 files:
Example of logging
41 lines of code changed in 1 file:
Example of lazy evaluation after tree change events.
27 lines of code changed in 1 file:
update ready for Marc to show me
90 lines of code changed in 1 file:
adding elements to store-restore
42 lines of code changed in 2 files:
small change
20 lines of code changed in 1 file:
Complete phase1
24 lines of code changed in 1 file:
working on summary - need to calculate "sigmoidal" medians, etc
85 lines of code changed in 1 file:
added the "tracer" analysis similar to EBSP
377 lines of code changed in 2 files:
Special logger
10 lines of code changed in 1 file:
like GibbsOperator --not the right thing to do but temporal solution
16 lines of code changed in 1 file:
just updating - need to see why infty in SliceSampler. It fails in Oldscore vs currentScore
2 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
85 lines of code changed in 1 file:
fixed coalescent interval in Likelihood suff. stat and small testing to Block Update
5 lines of code changed in 1 file:
Fixed updating the likelihood
9 lines of code changed in 1 file:
added prior of hyperparameters to "likelihood" wrong but functional, don't want to add a Parser for a mixture prior
17 lines of code changed in 1 file:
testing GPBlockUpdate -trying to understand Prior value
15 lines of code changed in 1 file:
small changes
48 lines of code changed in 1 file:
Created a new cleaner coalescent simulator parser to help generate nested subtrees from taxon sets. Updating BEAUti to generate simulated trees that conform to monophyly constrants and hard bounds on tmrcas.
1 lines of code changed in 2 files:
Porting 'evaluateLate' interface method from 1.7 branch.
4 lines of code changed in 2 files:
Fixed a (hopefully) final issue with sampling dates.
1 lines of code changed in 1 file:
Correct version of GMRF multilocus likelihood
268 lines of code changed in 1 file:
Not finished but descent version of GPOperator
44 lines of code changed in 1 file:
Finished Likelihood
46 lines of code changed in 1 file:
Updating Likelihood, need to add the GMRF part
119 lines of code changed in 1 file:
An odd import in this file (unused).
0 lines of code changed in 1 file:
updating small changes in operators and adding lambda_parameter
26 lines of code changed in 1 file:
updating Likelihood
20 lines of code changed in 1 file:
updating
24 lines of code changed in 1 file:
Commented changes - still revising
122 lines of code changed in 1 file:
this import breaks my build and is apparently not neccessary
1 lines of code changed in 1 file:
Moving parsers into release properties
281 lines of code changed in 1 file:
Editing mainly GPSLikelihoodParser
49 lines of code changed in 1 file:
Editing GaussianProcessSkytrackLikelihood.java and creating operators
68 lines of code changed in 1 file:
Creating GaussianProcessSkytrackLikelihood.java
233 lines of code changed in 1 file:
test
86 lines of code changed in 1 file:
test
1 lines of code changed in 1 file:
How annoying can I get with these commits?
1 lines of code changed in 1 file:
Saving GP likelihood again
1 lines of code changed in 1 file:
(167 more)