| Directory | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 170 (100.0%) | 9168 (100.0%) | 53.9 |
| src/dr/evomodel/epidemiology/casetocase/ | 141 (82.9%) | 8016 (87.4%) | 56.8 |
| src/dr/app/phylogeography/tools/ | 3 (1.8%) | 453 (4.9%) | 151.0 |
| src/test/dr/evomodel/substmodel/ | 4 (2.4%) | 264 (2.9%) | 66.0 |
| src/dr/inference/distribution/ | 4 (2.4%) | 224 (2.4%) | 56.0 |
| src/dr/inferencexml/distribution/ | 1 (0.6%) | 141 (1.5%) | 141.0 |
| / | 2 (1.2%) | 22 (0.2%) | 11.0 |
| src/dr/math/distributions/ | 2 (1.2%) | 21 (0.2%) | 10.5 |
| src/dr/app/beast/ | 11 (6.5%) | 18 (0.2%) | 1.6 |
| src/dr/inferencexml/model/ | 2 (1.2%) | 9 (0.1%) | 4.5 |
Bug fix
0 lines of code changed in 2 files:
More comments
0 lines of code changed in 4 files:
Minor fixes and comment changes
18 lines of code changed in 4 files:
efficiency improvements & other misc small fixes
24 lines of code changed in 7 files:
With the option -calculaterates this will now calculate mean Q matrix entries for all supported rates and give this in the text and KML files. Please test.
453 lines of code changed in 1 file:
Added simpler outbreak class (no latent periods).
616 lines of code changed in 4 files:
Now fairly confident geographical analysis has to be done in post-processing - removed.
13 lines of code changed in 2 files:
Added spatial kernel function; fixed bug.
107 lines of code changed in 2 files:
bug fixed
27 lines of code changed in 1 file:
bug fixed
31 lines of code changed in 1 file:
Done up to tracking down a few bugs
235 lines of code changed in 3 files:
Big and hopefully final rewrite
351 lines of code changed in 3 files:
C2CTL now implements treeTraitProvider and outputs painted trees
90 lines of code changed in 6 files:
Finished combining the classes.
23 lines of code changed in 3 files:
continuing the clean-up
422 lines of code changed in 2 files:
FC2CTL reworked to calculate overall likelihoods and randomly pick a transmission tree when MCMC samples are taken, similarly to discrete traits. Still probably too slow unless the likelihood function can be solved analytically. Will probably fold that class into the main C2CTL as a variant.
90 lines of code changed in 3 files:
Nomenclature change, continued
4 lines of code changed in 2 files:
Nomenclature change
508 lines of code changed in 7 files:
Tidying up
23 lines of code changed in 1 file:
Made the case class an inner class of the case set class, which is much neater.
294 lines of code changed in 5 files:
(40 more)