September 2008 Commit Log

Number of Commits:
26
Number of Active Developers:
6
msuchard 2008-09-30 09:15 Rev.: 1199

Damn class names. Who had the idea to name the Java classes as NativeX and the C files as X?

25 lines of code changed in 5 files:

msuchard 2008-09-30 06:30 Rev.: 1198

10 lines of code changed in 1 file:

msuchard 2008-09-30 06:16 Rev.: 1197

Added a native general likelihood core, an experimental likelihood core that holds partials/matrices/states as native pointers (intermediate step to off-loading these to the GPU).

1838 lines of code changed in 9 files:

jheled 2008-09-27 08:09 Rev.: 1196

comment added

6 lines of code changed in 2 files:

jheled 2008-09-27 08:07 Rev.: 1195

comment typo

5 lines of code changed in 1 file:

jheled 2008-09-27 08:07 Rev.: 1194

comment added

5 lines of code changed in 1 file:

jheled 2008-09-27 08:06 Rev.: 1193

spelling typo

6 lines of code changed in 1 file:

rambaut 2008-09-27 03:02 Rev.: 1192

Cleaning up

50 lines of code changed in 5 files:

msuchard 2008-09-26 08:27 Rev.: 1191

Sorry! My mistake re: TipPartialsModel.

425 lines of code changed in 1 file:

msuchard 2008-09-26 06:06 Rev.: 1190

Starting to merge GPU code into Beast. NOTE: TipPartialsModel is out-of-date vis-a-vis TreeLikelihood, so I commented out a line in TreeLikelihood

119 lines of code changed in 3 files:

msuchard 2008-09-24 06:50 Rev.: 1189

Started a new interface for BSSVS

51 lines of code changed in 4 files:

msuchard 2008-09-24 04:29 Rev.: 1188

Hacked minor round-off bug.

7 lines of code changed in 1 file:

Michael.DefoinPLatel 2008-09-18 23:43 Rev.: 1187

I added three operators for better mixing of rates with the autocorrelated model of rate of evolution

354 lines of code changed in 7 files:

Michael.DefoinPLatel 2008-09-18 22:08

423 lines of code changed in 2 files:

rambaut 2008-09-17 07:54 Rev.: 1184


832 lines of code changed in 1 file:

rambaut 2008-09-16 22:48 Rev.: 1183

Added an example file for the post-mortem damage (PMD) model

1561 lines of code changed in 1 file:

rambaut 2008-09-14 10:42 Rev.: 1182

Added the sequencing error/DNA damage model options to BEAUti.

1865 lines of code changed in 16 files:

rambaut 2008-09-14 09:13 Rev.: 1181

Added ability to select multiple traces in the load box of Tracer

175 lines of code changed in 3 files:

bloomquist 2008-09-09 11:53 Rev.: 1180

These are some files I have been working on for about 2 weeks. The only changes outisde of the GMRF stuff is a logHyperSphereVolume in MathUtils. It provides the log(volume) for a sphere in n dimensions with radius r.

926 lines of code changed in 10 files:

msuchard 2008-09-05 04:38 Rev.: 1179

Added colt.jar to zipgroup for beast.zip

3 lines of code changed in 1 file:

Sebastian.Hoehna 2008-09-03 17:53 Rev.: 1178

A new kind of tree proposal operators. Still working on it ...

1015 lines of code changed in 7 files:

Sebastian.Hoehna 2008-09-03 17:50 Rev.: 1177

Tests for the tree operators

931 lines of code changed in 8 files:

Sebastian.Hoehna 2008-09-03 17:44 Rev.: 1176

Some work on the tree operators.

182 lines of code changed in 10 files:

rambaut 2008-09-03 09:15 Rev.: 1175

bits and bobs

108 lines of code changed in 5 files:

msuchard 2008-09-03 04:48 Rev.: 1174

Implemented BSSVS for possible complex substitution matrices.

521 lines of code changed in 5 files:

msuchard 2008-09-01 09:12 Rev.: 1173

ComplexeSubstitutionModel will exponentiate any real matrix regardless if the infinitesimal generator contains complex eigenvalues (common in irreversible chains).

1231 lines of code changed in 4 files:

August 2008 »

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