December 2006 Commit Log

Number of Commits:
30
Number of Active Developers:
2
alexei.drummond 2006-12-18 11:18 Rev.: 116

message was incorrect

1 lines of code changed in 1 file:

alexei.drummond 2006-12-18 09:55 Rev.: 115

added option to parameterize rates as multipliers of parent rates rather than independent relative rates

17 lines of code changed in 1 file:

rambaut 2006-12-12 04:33 Rev.: 114

TRACER stuff

Andrew

920 lines of code changed in 8 files:

rambaut 2006-12-11 21:51 Rev.: 113

Fixed summarizing "changed" in TreeAnnotator

1 lines of code changed in 1 file:

rambaut 2006-12-07 01:55 Rev.: 112

Updated to better handle tip attributes.

Andrew

493 lines of code changed in 1 file:

alexei.drummond 2006-12-06 19:12 Rev.: 111

* Fixed SubtreeSlideOperator so that root node keeps the same trait and rate values if the old root is slid into the tree, or a internal node is slid above the root.
* Fixed RandomLocalClockModel to always return 0 for changed attribute for root node as there is no branch above it for a rate change to occur on.

44 lines of code changed in 4 files:

rambaut 2006-12-06 10:25 Rev.: 110

Fixed summarizing "changed" in TreeAnnotator

498 lines of code changed in 1 file:

rambaut 2006-12-06 03:38 Rev.: 109

A few tiny improvements.

6 lines of code changed in 2 files:

rambaut 2006-12-05 23:53 Rev.: 108

"changed" attribute from RandomLocalClockModel is now treated as binary (1, 0) and TreeAnnotator doesn't attempt to calculate HPDs, simply reports the proportion of 1s.

31 lines of code changed in 2 files:

rambaut 2006-12-05 23:30 Rev.: 107

Fixes to get everything compiling again

26 lines of code changed in 1 file:

alexei.drummond 2006-12-05 22:39 Rev.: 106

6 lines of code changed in 1 file:

rambaut 2006-12-05 22:17 Rev.: 105

Fixes to get everything compiling again

11 lines of code changed in 1 file:

rambaut 2006-12-05 22:08 Rev.: 104

Fixes to get everything compiling again

651 lines of code changed in 14 files:

alexei.drummond 2006-12-05 20:49 Rev.: 103

oops, fixed inadvertent compile error due to reversing some of my changes to TreeLikelihood in my last commit

1 lines of code changed in 1 file:

alexei.drummond 2006-12-05 17:52 Rev.: 102

further development of random local clocks model

237 lines of code changed in 5 files:

alexei.drummond 2006-12-05 13:07 Rev.: 101

fixing some of the errors caused by adding TreeAttributeProvider and NodeAttributeProvider...

60 lines of code changed in 4 files:

rambaut 2006-12-05 12:35 Rev.: 100

Added the "changed" attribute to those which TreeAnnotator averages.

1 lines of code changed in 1 file:

rambaut 2006-12-05 12:30 Rev.: 99

Improving tree logging

944 lines of code changed in 15 files:

rambaut 2006-12-05 11:38 Rev.: 98

I have removed the org.virion.jam package from the Trunk. This was the Java 1.4 version of JAM. The trunk now compiles against JEBL v0.3 which includes JAM and is based on Java 1.5. The jebl-0.3.jar can now be found in the lib/ folder.

44 lines of code changed in 3 files:

rambaut 2006-12-05 10:51 Rev.: 97

I have removed the org.virion.jam package from the Trunk. This was the Java 1.4 version of JAM. The trunk now compiles against JEBL v0.3 which includes JAM and is based on Java 1.5. The jebl-0.3.jar can now be found in the lib/ folder.

1 lines of code changed in 2 files:

rambaut 2006-12-05 10:08 Rev.: 96

RateEpochBranchRateModel working now. TreeModel.Node changed to have a more informative toString() which is nice for debugging in IntelliJ

28 lines of code changed in 3 files:

alexei.drummond 2006-12-05 09:53 Rev.: 95

error in exponentialPrior (issue 10) and new LocalBranchRates relaxed clock model

449 lines of code changed in 12 files:

rambaut 2006-12-05 04:36 Rev.: 94

Implemented a RateEpochBranchRateModel in which substitution rates are can vary amongst different epochs. This is for testing _a_priori_ hypotheses about changes in rate.

254 lines of code changed in 4 files:

rambaut 2006-12-05 02:35 Rev.: 93

Committed the latest version of Tracer (v1.4). This is a large rewrite, uses Java 1.5 and JEBL/JAM. The original Tracer (v1.3) remains in Branches/1.4

5919 lines of code changed in 64 files:

rambaut 2006-12-05 00:29 Rev.: 92

Some changes to dr.gui.chart to accommodate the new version of Tracer

272 lines of code changed in 7 files:

rambaut 2006-12-04 20:14 Rev.: 90

Issue 11 fix

1 lines of code changed in 1 file:

alexei.drummond 2006-12-04 17:53

error in exponentialPrior (issue 10)

44 lines of code changed in 2 files:

rambaut 2006-12-04 10:54 Rev.: 87

A few modifications from Marc's ARG branch

70 lines of code changed in 3 files:

rambaut 2006-12-04 09:59 Rev.: 84

Merged some more fixes and improvements I made in the 1.4 branch in to the trunk. Mostly changes to the TransmissionHistory classes. An update to AdvancedTreeLikelihood (I think only Beth uses this). XMLDocumentationHandler can handle integers now. TreeLogger can log TreeColourings more generically.

3032 lines of code changed in 10 files:

rambaut 2006-12-04 09:38 Rev.: 83

Merged some fixes and improvements I made in the 1.4 branch in to the trunk. This includes the fix for Issue 8 in LogCombiner. Also, I have made some interfaces in the TreeColouring stuff so that other sources of TreeColouring (such as the Transmission history stuff) can provide coloured trees for logging.

828 lines of code changed in 19 files:

November 2006 »

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