Lines of Code
[root]/src/dr/app/beauti/generator
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 1019 (100.0%) | 28789 (100.0%) | 28.2 |
| dong.w.xie | 647 (63.5%) | 15037 (52.2%) | 23.2 |
| alexei.drummond | 58 (5.7%) | 5789 (20.1%) | 99.8 |
| rambaut | 224 (22.0%) | 4343 (15.1%) | 19.3 |
| msuchard | 16 (1.6%) | 1951 (6.8%) | 121.9 |
| jheled | 37 (3.6%) | 706 (2.5%) | 19.0 |
| Michael.DefoinPLatel | 6 (0.6%) | 617 (2.1%) | 102.8 |
| dong.w.xie@gmail.com | 19 (1.9%) | 178 (0.6%) | 9.3 |
| fbielejec | 9 (0.9%) | 159 (0.6%) | 17.6 |
| Sibon.Li@gmail.com | 2 (0.2%) | 5 (0.0%) | 2.5 |
| bloomquist | 1 (0.1%) | 4 (0.0%) | 4.0 |
Leaf taxa are only added to a treeModel if it has them.
1 lines of code changed in 2 files:
Origin date needs its units set.
0 lines of code changed in 2 files:
Fixed that BEAUti was putting stateTagName attribute into TreeLikelihood elements (even though they should only be there for ancestralStateTreeLikelihoods). Was giving a parser warning when run (no other consequences).
6 lines of code changed in 2 files:
Added parsing and setting of date precisions in BEAUti plus generation of uniform sampling within these bounds. Also fixed the date calculations so Jan 1st (say 2013) is 2013.0.
58 lines of code changed in 3 files:
trunk: merge Issue 677
27 lines of code changed in 3 files:
trunk: merge Issue 677 : Using Microsatellite loci for inferring one phylogenetic tree that uses all the loci.
74 lines of code changed in 5 files:
BEAUti generates coalescent trees with matching opening and closing tags, a good property to have.
30 lines of code changed in 1 file:
Porting some fixes from 1.7 branch
5 lines of code changed in 3 files:
BEAUti now generates a hierarchical coalescent simulator that generates monophyletic groups and required clade heights. Clade heights can be given in the Taxon Sets table in the column called 'age'. These should lie inside any hard prior bounds (this is not done automatically).
28 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.
88 lines of code changed in 1 file:
trunk: merge Issue 656 : fix p=0 in Birth Death Serial Sampling Model, and update Unit tests.
5 lines of code changed in 2 files:
Porting fixes from 1.7.3 back into the trunk
66 lines of code changed in 10 files:
Fixed an issue with *BEAST 'species' attributes being left outside the taxon elements.
5 lines of code changed in 1 file:
Cleaned up the tipdate sampling options (the joint prior model wasn't generating code so hid this option). Removed requirement for taxon sets to be at least 2 taxa.
5 lines of code changed in 1 file:
Fix for http://code.google.com/p/beast-mcmc/issues/detail?id=620 - allows taxon sets of 1 taxon if 'includeStem' is selected.
13 lines of code changed in 1 file:
Fix for http://code.google.com/p/beast-mcmc/issues/detail?id=623. Logging multiple clock rates to tree logger now gives partition name prefixed tags.
49 lines of code changed in 1 file:
AncestralTreeLikelihood does not need a substitution model - it gets it from the site model.
0 lines of code changed in 1 file:
Fix for issue 625: http://code.google.com/p/beast-mcmc/issues/detail?id=625
TreeLikelihood for a non codon-partitioned partition was not being given the correct prefix if there was another codon-partitioned partition.
2 lines of code changed in 1 file:
attempt at fixing RC xml gen
13 lines of code changed in 1 file:
3 lines of code changed in 1 file:
Fixed an issue in BEAUti with robust counting XML generated where completely gapped sites were being stripped (these are sometimes used to maintain reading frame).
11 lines of code changed in 1 file:
Merged changes in 1.7 - fixes generation of MarkovJumps.
22 lines of code changed in 1 file:
trunk:solve Issue 589: BEAUti lost Uniform bound validation, and Issue 590: BEAUti prior dialog GUI logic bug
5 lines of code changed in 1 file:
trunk: merge Issue 577: BEAUti generator for *BEAST + calibrated Yule is broken
48 lines of code changed in 3 files:
trunk: merge Issue 579 and 580
6 lines of code changed in 1 file:
trunk: merge changes from branch 1.7
9 lines of code changed in 2 files:
Fix for issue 570.
1 lines of code changed in 1 file:
Cleaned up a the id labels for Discrete patterns.
11 lines of code changed in 1 file:
Fix for issue 568
The a partition prefix is now given if there is > 1 partition (plus some issues with the pattern lists inside merge patterns fixed - these don't now have ids).
3 lines of code changed in 1 file:
change confused method name and fix prefix bug inside mergePatterns
3 lines of code changed in 1 file:
fix a bug of taxa prefix
1 lines of code changed in 1 file:
trunk:solve Issue 548: Beauti does not generate functional xml for msat data analysis
4 lines of code changed in 2 files:
trunk:solve Issue 541: BEAUti generates wrong xml when enforcing a uniform prior on node ages, and add a nexus example with user specified starting tree
17 lines of code changed in 2 files:
reverting r4531
0 lines of code changed in 1 file:
Restored (but renamed to improve clarity) the UI to enable state counting other than the dNdS Robust Counting.
19 lines of code changed in 2 files:
should we add mergePatterns for dnds robust counting here?
3 lines of code changed in 1 file:
fixing dnds robust counting
38 lines of code changed in 2 files:
trunk:solve Issue 562: BEAUTi : Birth Death Epidemiology Model update
78 lines of code changed in 1 file:
trunk: remove wrong dependency to dr.evomodel.newtreelikelihood.TreeLikelihood which is not used by main BEAST
3 lines of code changed in 1 file:
trunk:solve Issue 558: duplicate method to check different taxa in BEAUti and Issue 557: Removing a partition doesn't remove its unique taxa
5 lines of code changed in 6 files:
(378 more)