August 2012 Commit Log

Number of Commits:
25
Number of Active Developers:
4
rambaut 2012-08-20 21:05 Rev.: 5148

Fix for Issue 660: For trait specification errors, error messages should include name of taxon.

8 lines of code changed in 1 file:

rambaut 2012-08-18 21:54 Rev.: 5145

If +Inf or NaN in MarkovChain, it now converts these to -Inf so it can continue if the user has chosen to ignore errors.

10 lines of code changed in 2 files:

msuchard 2012-08-18 06:32 Rev.: 5142

Due to lack of access to stochastic Dollo Alignment class to set printed ambiguity code, changing default ambiguity code to '-'.

2 lines of code changed in 1 file:

rambaut 2012-08-18 02:36 Rev.: 5141

Removing debug code...

14 lines of code changed in 1 file:

rambaut 2012-08-18 02:25 Rev.: 5139

Porting r5138 from 1.7 branch

16 lines of code changed in 1 file:

rambaut 2012-08-17 21:06 Rev.: 5137

Changed compound likelihood to return the actual special values (i.e. +Inf, NaN or -Inf) up the chain. Added 'todo' comment in MarkovChain suggesting a check for +Inf and NaN. Need to review this idea.

14 lines of code changed in 2 files:

rambaut 2012-08-16 03:27 Rev.: 5136

Porting r5135 from 1.7 branch

0 lines of code changed in 1 file:

rambaut 2012-08-15 22:34 Rev.: 5133

Porting changes 5131 and 5132 from 1.7 branch.

9 lines of code changed in 3 files:

dong.w.xie@gmail.com 2012-08-13 14:17 Rev.: 5129

trunk: merge Issue 656 : fix p=0 in Birth Death Serial Sampling Model, and update Unit tests.

51 lines of code changed in 8 files:

msuchard 2012-08-12 12:03 Rev.: 5124

Fixing thread pools: -1 = auto, 0 = single, >0 = pool

3 lines of code changed in 2 files:

rambaut 2012-08-11 08:53 Rev.: 5122

Fix for Issue 655: Operator log sometimes attempts to write to locked folder causing exception. Needs testing and porting to 1.7 branch.

35 lines of code changed in 5 files:

dong.w.xie@gmail.com 2012-08-10 13:05 Rev.: 5121

trunk: merge Issue 637: birth-death sampling model seems to not work smoothly

2 lines of code changed in 2 files:

danny.wilson@gmail.com 2012-08-09 04:56 Rev.: 5119

Submitting classes for epidemiological inference under deterministic SIS and SIR models to dr.evomodel.epidemiology

1454 lines of code changed in 9 files:

rambaut 2012-08-09 01:27 Rev.: 5118

Port from 1.7

2 lines of code changed in 2 files:

rambaut 2012-08-08 23:06 Rev.: 5116

Adding attributions.

12 lines of code changed in 10 files:

rambaut 2012-08-08 22:36 Rev.: 5114

Updated testBinaryDollo.xml to use new alsSiteModel parser.

3 lines of code changed in 2 files:

rambaut 2012-08-08 22:32 Rev.: 5113

Porting changes from branch 1.7 r5111 and r5112

176 lines of code changed in 6 files:

rambaut 2012-08-08 21:31 Rev.: 5110

Porting changes from branch 1.7 r5109

83 lines of code changed in 7 files:

rambaut 2012-08-08 10:19 Rev.: 5107

Porting 'evaluateLate' interface method from 1.7 branch.

206 lines of code changed in 35 files:

rambaut 2012-08-04 09:47 Rev.: 5100

Creating more consistent thread pool settings (-1 auto sizing thread pool, 0 thread pool off, >0 user-specified thread pool size).

12 lines of code changed in 3 files:

rambaut 2012-08-04 09:30 Rev.: 5098

Fixing default thread pool size back to 0 (which denotes an autosizing thread pool).

5 lines of code changed in 1 file:

rambaut 2012-08-04 03:49 Rev.: 5097

Porting fixes from 1.7.3 back into the trunk

448 lines of code changed in 52 files:

rambaut 2012-08-02 00:14 Rev.: 5081

Fix for Issue 643: Unable to specify a MRCA node to reconstruct ancestral states

5 lines of code changed in 1 file:

rambaut 2012-08-01 21:44 Rev.: 5080

Added test XML showing the tip date precision sampling.

478 lines of code changed in 1 file:

rambaut 2012-08-01 04:12 Rev.: 5079

Fixed a (hopefully) final issue with sampling dates.

7 lines of code changed in 3 files:

July 2012 »

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