| Directory | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 79 (100.0%) | 6154 (100.0%) | 77.8 |
| src/dr/app/beauti/options/ | 9 (11.4%) | 1220 (19.8%) | 135.5 |
| src/dr/app/beauti/ | 8 (10.1%) | 971 (15.8%) | 121.3 |
| src/dr/evomodel/clock/ | 23 (29.1%) | 930 (15.1%) | 40.4 |
| examples/ | 4 (5.1%) | 816 (13.3%) | 204.0 |
| src/dr/evomodel/operators/ | 5 (6.3%) | 658 (10.7%) | 131.6 |
| src/dr/app/beauti/generator/ | 6 (7.6%) | 617 (10.0%) | 102.8 |
| src/dr/inference/operators/ | 4 (5.1%) | 429 (7.0%) | 107.2 |
| src/dr/app/beast/ | 3 (3.8%) | 271 (4.4%) | 90.3 |
| src/dr/math/ | 2 (2.5%) | 113 (1.8%) | 56.5 |
| src/dr/evomodel/tree/ | 3 (3.8%) | 60 (1.0%) | 20.0 |
| src/dr/evomodel/branchratemodel/ | 2 (2.5%) | 27 (0.4%) | 13.5 |
| src/dr/app/tools/ | 1 (1.3%) | 12 (0.2%) | 12.0 |
| src/dr/inference/trace/ | 1 (1.3%) | 10 (0.2%) | 10.0 |
| src/dr/evolution/io/ | 1 (1.3%) | 10 (0.2%) | 10.0 |
| src/dr/evomodel/substmodel/ | 4 (5.1%) | 5 (0.1%) | 1.2 |
| native/ | 1 (1.3%) | 3 (0.0%) | 3.0 |
| src/dr/app/tracer/traces/ | 1 (1.3%) | 2 (0.0%) | 2.0 |
| src/dr/evoxml/ | 1 (1.3%) | 0 (0.0%) | 0.0 |
Replace the test file
366 lines of code changed in 1 file:
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).
211 lines of code changed in 12 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.
554 lines of code changed in 10 files:
Missing option for object file in Linux
3 lines of code changed in 1 file:
Started to integrate the autocorrelated relaxed clock in Beauti. Not happy yet with the intial priors. Some commented code will be removed later.
1749 lines of code changed in 8 files:
I added three operators for better mixing of rates with the autocorrelated model of rate of evolution
354 lines of code changed in 7 files:
423 lines of code changed in 2 files:
Fix a bug with the scaleAllIndependently option. The Hastings ratio was not computed properly. I can't figure out how bad it was... Please note that I rely on the existing formulla and I am not sure if this one is correct !
236 lines of code changed in 1 file:
Some improvements for mixing with relaxed clock models
1 lines of code changed in 1 file:
Some improvements for mixing with relaxed clock models
452 lines of code changed in 6 files:
Allow treeTraceAnalysis to check if a reference tree is present in the credible set (using the shortReport mehtod only)
59 lines of code changed in 2 files:
Extend the model to allow the number of effective categories to be different from the number of branches + bug fix (the rightmost quantile was never used)
26 lines of code changed in 1 file:
Bug fix
113 lines of code changed in 1 file:
Allow optional upper and lower. If optional then the boundaries are obtained directly from the parameter.
15 lines of code changed in 1 file:
Restore TruncNormalDistribution
41 lines of code changed in 1 file:
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:
Add an option in LogAnalyser to export the standard error
22 lines of code changed in 2 files:
Display the log likelihood and all negative numbers in decimal format
2 lines of code changed in 1 file:
Two missing files added.
0 lines of code changed in 2 files:
(1 more)