February 2007 Commit Log

Number of Commits:
16
Number of Active Developers:
4
alexei.drummond 2007-02-28 15:01 Rev.: 209

comment on temperature parameter in acceptance code

9 lines of code changed in 2 files:

msuchard 2007-02-23 12:36 Rev.: 208

Added MrBayesDefaultModel as a speciation model. This class puts an Exponential prior on the rootHeight and assumes all branch lengths are uniform given the root. For the model to run, I modified ScaledOperator as one can specify how many degrees of freedom are actually scaled for the Hastings ratio ( = 1, only the rootHeight, under the MrBayesDefaultModel when scaling all node heights simultaneously). Also, I modifed SubtreeSlideOperator so that it does not change the rootHeight when branchesAreScaledAsDirichlet="true" is set. Someone still needs to work out the Hastings ratio under the MrBayesDefaultModel when the rootHeight changes in the SubtreeSlideOperator. A good grad student exercise?

508 lines of code changed in 4 files:

msuchard 2007-02-18 12:15 Rev.: 207

Added a Gamma random variable sampler to the MersenneTwisterFast and MathUtils classes. The function nextGamma(alpha, lambda) should generate RVs with expectation alpha / lambda and variance alpha / lambda^2. Needs to be double-checked,

925 lines of code changed in 2 files:

rambaut 2007-02-12 09:57 Rev.: 205

added link to jebl library in ant build file

1 lines of code changed in 1 file:

alexei.drummond 2007-02-11 10:07 Rev.: 204

Fix for issue 15

1 lines of code changed in 1 file:

rambaut 2007-02-08 10:04 Rev.: 203

Made a start on implementing RandomLocalClocks in BEAUti. It is all there but I haven't tested the XML that is generated.

2278 lines of code changed in 7 files:

alexei.drummond 2007-02-07 16:30 Rev.: 202

A work in progress -- this book section is for the new edition of "The Phylogenetic Handbook". It should make for the start of a very nice manual when it is finished as well.

707 lines of code changed in 4 files:

jheled 2007-02-05 13:25 Rev.: 200

correct element name

2 lines of code changed in 1 file:

jheled 2007-02-05 13:24 Rev.: 199

swap only 1-0 pairs. mathematically correct now (i hope)

62 lines of code changed in 1 file:

jheled 2007-02-05 11:54 Rev.: 198

partial generification

7 lines of code changed in 1 file:

jheled 2007-02-05 11:13 Rev.: 197

partial generification

3 lines of code changed in 1 file:

rambaut 2007-02-02 00:46 Rev.: 192

Added dr/gui/table which contains a few classes used by some of the GUI apps that are not in the JEBL library

1821 lines of code changed in 6 files:

jheled 2007-02-01 13:23 Rev.: 191

correct error message

3 lines of code changed in 1 file:

jheled 2007-02-01 13:22 Rev.: 190

fix buggy code which results in incorrect evaluation and negative population sizes

14 lines of code changed in 2 files:

jheled 2007-02-01 13:20 Rev.: 189

report error with incomplete tree

3 lines of code changed in 1 file:

alexei.drummond 2007-02-01 09:37 Rev.: 188

added the facility for a clock.rate parameter in the random local clocks model so that a mean rate across all local clocks can be specified for the purposes of fossil-calibrated analyses. Untested :-)

16 lines of code changed in 3 files:

January 2007 »

Generated by StatSVN 0.7.0