January 2009 Commit Log

Number of Commits:
15
Number of Active Developers:
3
msuchard 2009-01-31 05:46 Rev.: 1414

Fixing bugs in ComplexSubstitutionModel

362 lines of code changed in 5 files:

bloomquist 2009-01-28 13:33 Rev.: 1413

Fixed bug when Alexei added in variable stuff to parameter changed events. Our GMRFSkyrideLikelihood never handled these new events.

3 lines of code changed in 1 file:

rambaut 2009-01-15 00:25 Rev.: 1412

Updated version number

3 lines of code changed in 1 file:

rambaut 2009-01-15 00:23 Rev.: 1411

Rearranged the check for difficult intervals to avoid a divide by zero when intervalArea is zero.

2 lines of code changed in 1 file:

rambaut 2009-01-15 00:06 Rev.: 1410

Added a 'getThreshold' method to the DemographicFunction which gets passed on to the calculate likelihood function. This defaults to zero in DemographicFunction. Abstract but is 1E-12 in VDdemographicFunction.

18 lines of code changed in 3 files:

bloomquist 2009-01-13 10:35 Rev.: 1409

Three example arg datasets.

10494 lines of code changed in 3 files:

rambaut 2009-01-13 08:11 Rev.: 1408

Put back in the underflow? check at Joseph's request.

2 lines of code changed in 1 file:

rambaut 2009-01-13 08:06 Rev.: 1407

Added an optional 'threshold' on the static method 'calculateLogLikelihood' to allow for a check for ill-conditioned coalescent intervals. A static method with the old signature calls this with a zero threshold (i.e., no check). This just moves the problem up to CoalescentLikelihood which calls this static method.

11 lines of code changed in 1 file:

rambaut 2009-01-13 03:15 Rev.: 1406

Removed an (underflow?) check in calculating the coalescent likelihood. This was preventing a big initial tree from being calculated. The warning message is still going to be written to see if there is a long term problem.

9 lines of code changed in 1 file:

rambaut 2009-01-10 10:28 Rev.: 1405

Created a new parser called 'patternSubSet' which takes a SiteList (which includes Alignments and SitePatters) and creates a subset.

2 lines of code changed in 1 file:

rambaut 2009-01-10 05:23 Rev.: 1404

Fixed problem generating XML to sample from the prior in BEAUti.

46 lines of code changed in 4 files:

bloomquist 2009-01-07 15:19 Rev.: 1403

Ok, I think I got it! This one actually sampled correctly.

25 lines of code changed in 1 file:

bloomquist 2009-01-07 13:16 Rev.: 1402

Let in some debug stuff on accident.

5 lines of code changed in 1 file:

bloomquist 2009-01-07 13:05 Rev.: 1401

Made major fix to ARGAddRemoveOperator.

717 lines of code changed in 6 files:

rambaut 2009-01-01 04:06 Rev.: 1400

Refactored the guess dates dialog into a stand-alone class with concomitant simplification in the calling code. Added a 'regex' option for guessing dates.

254 lines of code changed in 4 files:

December 2008 »

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