November 2006 Commit Log

Number of Commits:

8

Number of Active Developers:

5

benjamin.redelings 2006-11-16 11:05 #8 Rev.: 75

[SPEED] Calculate ESS faster in Tracer and LogAnalyzer

* src/dr/app/tracer/TraceCorrelation.java
+ analyseCorrelation( )
- merge stopping criterion into loop calculation of gammaStat[]
- for Tracer

* src/dr/inference/trace/TraceAnalysis.java
+ analyze( )
- merge stopping criterion into loop calculation of gammaStat[]
- for LogAnalyzer

This change makes the required CPU time less dependant on MAX_OFFSET.

54 lines of code changed in 2 files:

• src/dr/app/tracer: TraceCorrelation.java (+29 -23)
• src/dr/inference/trace: TraceAnalysis.java (+25 -23)

sidneym 2006-11-10 16:35 #7 Rev.: 74

remove subdirectory created by mistake

0 lines of code changed in 1 file:

• trunk (del)

msuchard 2006-11-09 16:03 #6 Rev.: 71

Ancestral recombination graph branch

0 lines of code changed in 1 file:

• trunk (new)

rambaut 2006-11-03 23:32 #5 Rev.: 68

Small adjustment to parameter log order.

2 lines of code changed in 1 file:

• src/dr/app/beauti: BeastGenerator.java (+2 -3)

rambaut 2006-11-03 23:24 #4 Rev.: 67

Altered order of parameters in log files as described in a recent posting. Added a few more lines of feedback to LogCombiner.

330 lines of code changed in 2 files:

• src/dr/app/beauti: BeastGenerator.java (+75 -66)
• src/dr/app/tools: LogCombiner.java (+255 -247)

alexei.drummond 2006-11-03 13:07 #3 Rev.: 66

fixed license headers

258 lines of code changed in 10 files:

• src/dr/app/coalgen: CoalGenApp.java (+27 -8), CoalGenData.java (+26 -8), CoalGenFrame.java (+27 -6), CoalGenMenuFactory.java (+28 -6), DataPanel.java (+27 -7), ModelPanel.java (+27 -9), Trace.java (new 24), TraceException.java (new 24), TraceList.java (new 24), Traces.java (new 24)

alexei.drummond 2006-11-03 12:53 #2 Rev.: 65

Added coalgen application back into the mix (after getting it compiling and running again)

1801 lines of code changed in 16 files:

• src/dr/app/coalgen: CoalGenApp.java (+57), CoalGenData.java (+264), CoalGenFrame.java (+323), CoalGenMenuFactory.java (+39), DataPanel.java (+569), ModelPanel.java (+193), Trace.java (+72), TraceException.java (+16), TraceList.java (+40), Traces.java (+225)
• src/dr/app/coalgen/images: CoalGen.png (new), add.png (new), exclude.png (new), include.png (new), minus.png (new)
• src/dr/inference/trace: TraceAnalysis.java (+3 -3)

rambaut 2006-11-03 02:49 #1 Rev.: 64

A few new stats in TreeStat (probably not much use to most people).

184 lines of code changed in 4 files:

• src/dr/app/treestat: StatisticsPanel.java (+9 -4)
• src/dr/app/treestat/statistics: LineageCountStatistic.java (+4 -4), LineageProportionStatistic.java (+86), MRCAOlderThanStatistic.java (+85)

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