Lines of Code
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 184 (100.0%) | 4531 (100.0%) | 24.6 |
| rambaut | 50 (27.2%) | 1699 (37.5%) | 33.9 |
| jheled | 72 (39.1%) | 873 (19.3%) | 12.1 |
| alexei.drummond | 18 (9.8%) | 823 (18.2%) | 45.7 |
| alexander.alekseyenko | 5 (2.7%) | 406 (9.0%) | 81.2 |
| msuchard | 10 (5.4%) | 372 (8.2%) | 37.2 |
| dong.w.xie | 24 (13.0%) | 315 (7.0%) | 13.1 |
| akaruiws | 2 (1.1%) | 23 (0.5%) | 11.5 |
| julia.pal.r@gmail.com | 1 (0.5%) | 16 (0.4%) | 16.0 |
| dong.w.xie@gmail.com | 2 (1.1%) | 4 (0.1%) | 2.0 |
Added MPI ranking of output for embarrassingly parallel use on Keeneland.
16 lines of code changed in 2 files:
Fix for Issue 655: Operator log sometimes attempts to write to locked folder causing exception. Needs testing and porting to 1.7 branch.
24 lines of code changed in 1 file:
Corrected spelling and simplified error XML reporting (commented out public ID and System ID).
3 lines of code changed in 1 file:
Reverting inadvertent changes from Julia
25 lines of code changed in 2 files:
Not finished but descent version of GPOperator - fixing imports :S
16 lines of code changed in 1 file:
trunk: merge the change of BEAST parser doc
4 lines of code changed in 2 files:
trunk:solve Issue 481: Improve reporting of XML errors
41 lines of code changed in 1 file:
Fixed a few issues with parsing string arrays.
5 lines of code changed in 4 files:
Added ability to extract individual virus locations as statistics.
2 lines of code changed in 1 file:
Upgraded chain length to a 64 bit integer so that chain lengths > 2.1 billion can be done. This addresses issue 540. Runs OK, accepts long chain lengths but not actually tested a run of > 2.1 billion.
32 lines of code changed in 2 files:
uncommitting an erroneous revision
0 lines of code changed in 2 files:
Add functionality to read plink SNP frequencies and run continuous diffusion models
44 lines of code changed in 1 file:
Trunk: make Integer Parameter to allow to pass Variable<Integer>.
1 lines of code changed in 1 file:
Trunk: solve Issue 370: BEAST argument -overwrite not working
2 lines of code changed in 1 file:
Added command line option '-prefix <PREFIX>' to specify a string which will be prefixed to all output log files. This is an alternative to changing the log file names in the XML when running multiple replicate runs in the same location.
12 lines of code changed in 1 file:
LoggerParser uses a special function to get the log file which may set different paths (for example to a working directory). Thus just checking that fileName exists may not work. So moved the check for existing file into XMLParser.getFilePrintWriter(). This has the added benefit that all loggers use this function and thus all have the overwriting behaviour.
Also added a check box to the BEAST options dialog box.
20 lines of code changed in 1 file:
Started to implement a branch rate model that takes a realization of a discrete location provided by a MarkovJumpsTreeLikelihood and produces a continuous diffusion rate based on the proportion of time spent in each location and a vector of relative rates and indicators. Builds but not finished implementing.
3 lines of code changed in 1 file:
TRUNK: merge Issue 291 from branch 1.5.
40 lines of code changed in 2 files:
Trunk refactoring: fix a bug of duplcation parser name in GMRF Skyride Likelihood.
6 lines of code changed in 1 file:
Trunk: merge r2712
9 lines of code changed in 4 files:
Trunk: merge r2700
42 lines of code changed in 2 files:
Trunk: start merge parser from branch 1.5 in
43 lines of code changed in 3 files:
Further improvement of BEAST parser doc
2 lines of code changed in 1 file:
Making better BeastParserDoc.
20 lines of code changed in 2 files:
Solve Issue 227: Fix BeastDoc to generate tag doc for BEAST users, but need enhancement.
102 lines of code changed in 4 files:
Implemented checks to see that all models, likelihood and parameters are being controlled by the MCMC. The checks are made in MCMCParser but the warnings are currently commented out.
25 lines of code changed in 2 files:
BEAUTi: solve Issue 155: Warning message " ... does not match stored object with same id and tag name ..." confused user.
5 lines of code changed in 1 file:
generify and auto intelliJ
2 lines of code changed in 2 files:
auto intelliJ
3 lines of code changed in 1 file:
code police
1 lines of code changed in 2 files:
xml warnings - my previous attempt was incomplete as expected. hopfully this is better
78 lines of code changed in 12 files:
comments added
2 lines of code changed in 1 file:
code police
21 lines of code changed in 2 files:
Added more checking for spurios elements, e.g.
<strictClockBranchRates id="branchRates">
<rate>
<blu/>
<parameter id="clock.rate" value="1.0"/>
<bla/>
</rate>
</strictClockBranchRates>
Please report back if you encounter erroneous reports
47 lines of code changed in 1 file:
23 lines of code changed in 2 files:
Beginning of refactoring to remove dr.inference.* dependency on dr.xml. Will take a while...
77 lines of code changed in 3 files:
refactoring to remove illegal dependencies (dr.inference should not depend on dr.evo*.*) and tidying
45 lines of code changed in 3 files:
Refactoring tidy up. Reducing interdependencies between top-level packages. Will upload dependency guidelines to wiki soon.
42 lines of code changed in 3 files:
tidying up some of the example files -- the eventual aim is for the tag names for id/idref pairs to always match for consistency, and enhanced ability to use standard parsing tools such as XMLSchema et cetera. At the moment I have modified XMLParser so that it just prints a warning to stderr unless strictXML is turned on, in which case an XMLParserException is thrown when the tag names of an id/idref pair don't match.
81 lines of code changed in 4 files:
adding the files missing from r1812
359 lines of code changed in 3 files:
(53 more)