| Directory | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 2136 (100.0%) | 153136 (100.0%) | 71.6 |
| doc/ | 40 (1.9%) | 15648 (10.2%) | 391.2 |
| src/dr/geo/ | 100 (4.7%) | 9239 (6.0%) | 92.3 |
| src/dr/evomodel/tree/ | 77 (3.6%) | 7296 (4.8%) | 94.7 |
| src/dr/evomodel/substmodel/ | 81 (3.8%) | 6122 (4.0%) | 75.5 |
| src/dr/app/beauti/generator/ | 58 (2.7%) | 5789 (3.8%) | 99.8 |
| src/dr/evomodel/arg/ | 21 (1.0%) | 4897 (3.2%) | 233.1 |
| src/dr/app/beauti/ | 88 (4.1%) | 4876 (3.2%) | 55.4 |
| src/dr/evomodel/coalescent/ | 82 (3.8%) | 4697 (3.1%) | 57.2 |
| src/dr/app/beauti/options/ | 104 (4.9%) | 4525 (3.0%) | 43.5 |
| src/dr/inference/model/ | 89 (4.2%) | 4451 (2.9%) | 50.0 |
| src/dr/evomodel/operators/ | 53 (2.5%) | 4146 (2.7%) | 78.2 |
| src/dr/inference/operators/ | 80 (3.7%) | 3997 (2.6%) | 49.9 |
| src/dr/evolution/tree/ | 32 (1.5%) | 3932 (2.6%) | 122.8 |
| src/dr/app/tools/ | 25 (1.2%) | 3771 (2.5%) | 150.8 |
| src/dr/evomodel/speciation/ | 87 (4.1%) | 3748 (2.4%) | 43.0 |
| examples/ | 48 (2.2%) | 3636 (2.4%) | 75.7 |
| src/dr/math/distributions/ | 23 (1.1%) | 3232 (2.1%) | 140.5 |
| src/dr/app/coalgen/ | 34 (1.6%) | 3119 (2.0%) | 91.7 |
| examples/treePriors/ | 26 (1.2%) | 2712 (1.8%) | 104.3 |
| src/dr/inference/distribution/ | 65 (3.0%) | 2656 (1.7%) | 40.8 |
| src/dr/app/tracer/analysis/ | 22 (1.0%) | 2636 (1.7%) | 119.8 |
| src/dr/evomodel/arg/operators/ | 9 (0.4%) | 2472 (1.6%) | 274.6 |
| src/dr/inference/trace/ | 39 (1.8%) | 2412 (1.6%) | 61.8 |
| src/dr/evomodel/continuous/ | 39 (1.8%) | 2408 (1.6%) | 61.7 |
| src/dr/evomodel/branchratemodel/ | 61 (2.9%) | 1997 (1.3%) | 32.7 |
| src/dr/evolution/io/ | 11 (0.5%) | 1655 (1.1%) | 150.4 |
| src/dr/evomodel/treelikelihood/ | 38 (1.8%) | 1578 (1.0%) | 41.5 |
| src/dr/gui/chart/ | 18 (0.8%) | 1404 (0.9%) | 78.0 |
| src/dr/app/beauti/priorsPanel/ | 11 (0.5%) | 1324 (0.9%) | 120.3 |
| src/dr/evomodelxml/ | 20 (0.9%) | 1315 (0.9%) | 65.7 |
| src/dr/app/tracer/traces/ | 23 (1.1%) | 1166 (0.8%) | 50.6 |
| src/test/dr/evomodel/substmodel/ | 17 (0.8%) | 1163 (0.8%) | 68.4 |
| examples/Phylogeography/ | 1 (0.0%) | 1162 (0.8%) | 1162.0 |
| src/dr/evolution/datatype/ | 17 (0.8%) | 1134 (0.7%) | 66.7 |
| src/dr/evolution/alignment/ | 7 (0.3%) | 1001 (0.7%) | 143.0 |
| src/dr/evomodel/sitemodel/ | 16 (0.7%) | 975 (0.6%) | 60.9 |
| src/dr/app/beast/ | 38 (1.8%) | 949 (0.6%) | 24.9 |
| src/dr/app/treestat/statistics/ | 10 (0.5%) | 935 (0.6%) | 93.5 |
| src/dr/math/ | 35 (1.6%) | 924 (0.6%) | 26.4 |
| src/dr/inferencexml/ | 6 (0.3%) | 920 (0.6%) | 153.3 |
| src/dr/app/beauti/modelsPanel/ | 8 (0.4%) | 909 (0.6%) | 113.6 |
| src/dr/app/tracer/application/ | 4 (0.2%) | 853 (0.6%) | 213.2 |
| src/dr/evolution/colouring/ | 7 (0.3%) | 830 (0.5%) | 118.5 |
| examples/calibrations/ | 9 (0.4%) | 827 (0.5%) | 91.8 |
| src/dr/xml/ | 18 (0.8%) | 823 (0.5%) | 45.7 |
| src/dr/evolution/coalescent/ | 13 (0.6%) | 791 (0.5%) | 60.8 |
| src/dr/evomodel/coalescent/operators/ | 11 (0.5%) | 737 (0.5%) | 67.0 |
| src/dr/inference/loggers/ | 28 (1.3%) | 684 (0.4%) | 24.4 |
| src/dr/inference/mcmc/ | 13 (0.6%) | 652 (0.4%) | 50.1 |
| src/dr/evoxml/ | 27 (1.3%) | 648 (0.4%) | 24.0 |
| src/dr/stats/ | 3 (0.1%) | 643 (0.4%) | 214.3 |
| src/dr/util/ | 10 (0.5%) | 629 (0.4%) | 62.9 |
| src/test/dr/evomodel/speciation/ | 18 (0.8%) | 612 (0.4%) | 34.0 |
| src/dr/app/vcs/ | 9 (0.4%) | 576 (0.4%) | 64.0 |
| src/dr/evomodel/randomYule/ | 8 (0.4%) | 540 (0.4%) | 67.5 |
| doc/StarBEAST/ | 4 (0.2%) | 529 (0.3%) | 132.2 |
| / | 10 (0.5%) | 515 (0.3%) | 51.5 |
| src/dr/evomodel/indel/ | 8 (0.4%) | 479 (0.3%) | 59.8 |
| src/dr/evomodel/arg/coalescent/ | 5 (0.2%) | 475 (0.3%) | 95.0 |
| src/dr/evomodel/MSSD/ | 14 (0.7%) | 415 (0.3%) | 29.6 |
| src/dr/evomodel/tree/randomlocalmodel/ | 5 (0.2%) | 412 (0.3%) | 82.4 |
| src/dr/evolution/coalescent/structure/ | 8 (0.4%) | 404 (0.3%) | 50.5 |
| src/dr/evolution/sequence/ | 4 (0.2%) | 363 (0.2%) | 90.7 |
| src/dr/inference/markovchain/ | 5 (0.2%) | 357 (0.2%) | 71.4 |
| src/dr/evomodel/transmission/ | 10 (0.5%) | 339 (0.2%) | 33.9 |
| examples/beauti1.5/treePrior+clockModel/ | 2 (0.1%) | 327 (0.2%) | 163.5 |
| src/dr/evolution/distance/ | 6 (0.3%) | 322 (0.2%) | 53.6 |
| doc/BookSection/ | 2 (0.1%) | 308 (0.2%) | 154.0 |
| src/dr/app/beastdev/ | 13 (0.6%) | 273 (0.2%) | 21.0 |
| src/dr/evomodel/newtreelikelihood/ | 4 (0.2%) | 263 (0.2%) | 65.7 |
| src/dr/evomodel/coalescent/structure/ | 19 (0.9%) | 252 (0.2%) | 13.2 |
| src/dr/app/beauti/util/ | 4 (0.2%) | 252 (0.2%) | 63.0 |
| src/test/dr/evomodel/operators/ | 4 (0.2%) | 248 (0.2%) | 62.0 |
| src/dr/evomodel/arg/likelihood/ | 4 (0.2%) | 247 (0.2%) | 61.7 |
| src/dr/evolution/wrightfisher/ | 6 (0.3%) | 240 (0.2%) | 40.0 |
| src/dr/evomodel/clock/ | 19 (0.9%) | 225 (0.1%) | 11.8 |
| src/dr/app/pathogen/ | 5 (0.2%) | 212 (0.1%) | 42.4 |
| src/dr/app/oldbeauti/ | 7 (0.3%) | 206 (0.1%) | 29.4 |
| src/dr/inference/xml/ | 2 (0.1%) | 192 (0.1%) | 96.0 |
| src/dr/evomodel/beagle/substmodel/ | 16 (0.7%) | 189 (0.1%) | 11.8 |
| src/dr/evomodelxml/speciation/ | 10 (0.5%) | 188 (0.1%) | 18.8 |
| src/dr/evomodel/arg/branchratemodel/ | 3 (0.1%) | 168 (0.1%) | 56.0 |
| src/dr/app/ | 2 (0.1%) | 146 (0.1%) | 73.0 |
| src/test/dr/distibutions/ | 3 (0.1%) | 139 (0.1%) | 46.3 |
| src/dr/inference/tutorial/ | 3 (0.1%) | 126 (0.1%) | 42.0 |
| src/dr/inference/prior/ | 3 (0.1%) | 114 (0.1%) | 38.0 |
| src/dr/inference/mcmcmc/ | 2 (0.1%) | 104 (0.1%) | 52.0 |
| src/test/dr/evomodel/treelikelihood/ | 1 (0.0%) | 103 (0.1%) | 103.0 |
| src/dr/inference/parallel/ | 2 (0.1%) | 92 (0.1%) | 46.0 |
| src/dr/app/beauti/traitspanel/ | 1 (0.0%) | 86 (0.1%) | 86.0 |
| src/test/dr/calibration/ | 2 (0.1%) | 83 (0.1%) | 41.5 |
| src/dr/app/beauti/datapanel/ | 1 (0.0%) | 75 (0.0%) | 75.0 |
| src/dr/app/beauti/mcmcpanel/ | 1 (0.0%) | 71 (0.0%) | 71.0 |
| src/dr/exporters/ | 4 (0.2%) | 70 (0.0%) | 17.5 |
| src/dr/ | 1 (0.0%) | 70 (0.0%) | 70.0 |
| src/dr/gui/ | 4 (0.2%) | 64 (0.0%) | 16.0 |
| src/dr/evomodelxml/operators/ | 1 (0.0%) | 64 (0.0%) | 64.0 |
| src/dr/evolution/parsimony/ | 1 (0.0%) | 61 (0.0%) | 61.0 |
| src/dr/app/util/ | 1 (0.0%) | 57 (0.0%) | 57.0 |
| src/dr/app/beauti/treespanel/ | 1 (0.0%) | 54 (0.0%) | 54.0 |
| src/dr/evomodel/ibd/ | 6 (0.3%) | 49 (0.0%) | 8.1 |
| src/dr/app/treestat/ | 7 (0.3%) | 49 (0.0%) | 7.0 |
| src/dr/app/seqgen/ | 2 (0.1%) | 48 (0.0%) | 24.0 |
| release/ | 2 (0.1%) | 38 (0.0%) | 19.0 |
| src/dr/geo/cartogram/ | 3 (0.1%) | 36 (0.0%) | 12.0 |
| src/test/dr/inference/ | 1 (0.0%) | 32 (0.0%) | 32.0 |
| src/test/dr/app/beauti/ | 1 (0.0%) | 26 (0.0%) | 26.0 |
| src/dr/evomodel/beagle/sitemodel/ | 4 (0.2%) | 16 (0.0%) | 4.0 |
| src/dr/matrix/ | 2 (0.1%) | 15 (0.0%) | 7.5 |
| src/dr/app/beauti/tipdatepanel/ | 1 (0.0%) | 13 (0.0%) | 13.0 |
| release/common/ | 1 (0.0%) | 13 (0.0%) | 13.0 |
| src/dr/app/beauti/taxonsetspanel/ | 1 (0.0%) | 11 (0.0%) | 11.0 |
| src/dr/evomodel/newsubstmodel/ | 5 (0.2%) | 9 (0.0%) | 1.8 |
| src/dr/app/beauti/operatorspanel/ | 1 (0.0%) | 9 (0.0%) | 9.0 |
| src/dr/app/phylogeography/builder/ | 1 (0.0%) | 7 (0.0%) | 7.0 |
| src/test/dr/evomodel/arg/operators/ | 1 (0.0%) | 6 (0.0%) | 6.0 |
| src/dr/evomodel/beagle/treelikelihood/ | 2 (0.1%) | 3 (0.0%) | 1.5 |
| doc/tutorial/DivergenceDating/1.2_Primates/latex/ | 4 (0.2%) | 3 (0.0%) | 0.7 |
| src/dr/app/misc/ | 1 (0.0%) | 1 (0.0%) | 1.0 |
| src/dr/gui/table/images/ | 2 (0.1%) | 0 (0.0%) | 0.0 |
| src/dr/gui/table/ | 2 (0.1%) | 0 (0.0%) | 0.0 |
| src/dr/evolution/geo/ | 6 (0.3%) | 0 (0.0%) | 0.0 |
| src/dr/app/coalgen/images/ | 5 (0.2%) | 0 (0.0%) | 0.0 |
| lib/ | 4 (0.2%) | 0 (0.0%) | 0.0 |
| doc/Virus Practical Tex/ | 1 (0.0%) | 0 (0.0%) | 0.0 |
Rearranging code in SeqGen to speed it up a bit for very large trees (100,000 tips)
5 lines of code changed in 1 file:
Added warning about single-child internal nodes that is suppressed in TreeStat but active in BEAST-MCMC and other programs.
14 lines of code changed in 3 files:
Added SingleChildCountStatistic to TreeStat to support e.g. the counting of direct ancestors and nodes representing migration events.
91 lines of code changed in 3 files:
Relaxed nexus importer to allow internal nodes with 1 or more children. This is to allow TreeStat to analyze direct ancestor trees and migration trees where migrations events are defined by internal nodes.
11 lines of code changed in 1 file:
Added a hack to get rough time-tree out of Pathogen
59 lines of code changed in 3 files:
fixed microsatellite initial value errors in geomDist and propLinear parameters (if in doubt, shouldn't start on boundary values as a general rule).
2 lines of code changed in 1 file:
wording change
3 lines of code changed in 4 files:
fixed random seed
6 lines of code changed in 2 files:
added parser for IntermediateExchange.
64 lines of code changed in 1 file:
added handling for multi-block partitions
191 lines of code changed in 4 files:
added Beta Diversity statistic to Tree Stat
27 lines of code changed in 3 files:
added Beta Diversity statistic to Tree Stat
175 lines of code changed in 2 files:
parser fix
4 lines of code changed in 2 files:
Tidied up parsers and added option to specify epoch widths from the origin rather than the tips.
61 lines of code changed in 5 files:
likelihoods correct! phew! Late night debugging with Denise and Tanja in Zurich ;-)
308 lines of code changed in 3 files:
removed final time interval
1 lines of code changed in 1 file:
removed final time interval
45 lines of code changed in 2 files:
20 taxa, 7 constraints, 0.1seconds
16 lines of code changed in 2 files:
yes
228 lines of code changed in 3 files:
count constrained ranked trees
231 lines of code changed in 1 file:
(295 more)