/trunk Developers: benjamin.redelings

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benjamin.redelings 2009-10-17 04:50 Rev.: 2430

[NEW] Add a site model with free rate parameters.
It doesn't actually work yet, for some reason...

* dr/app/beast/development_parses.properties:
+ Add DirichletSiteModel
* src/dr/evomodel/sitemodel/DirichletSiteModel.java
+ New model class.

314 lines of code changed in 2 files:

• src/dr/app/beast: development_parsers.properties (+3 -1)
• src/dr/evomodel/sitemodel: DirichletSiteModel.java (+311)

benjamin.redelings 2009-10-15 04:33 Rev.: 2398

[NEW] Really compute effective sample size of combined Traces

* app/tracer/traces/CombinedTraces.java
+ class CombinedTraces
- TraceDistribution[] traceStatistics: change type to TraceCorrelation
- getDistributionStatistics( )
+ Just call getCorrelationStatistics( )
- getCorrelationStatistics( )
+ return our cached TraceCorrelation object
- analyseTrace( )
+ Just compute a TraceCorrelation object from the concatenated values.

15 lines of code changed in 1 file:

• src/dr/app/tracer/traces: CombinedTraces.java (+15 -22)

benjamin.redelings 2009-10-05 05:25 Rev.: 2345

* build.xml
+ update to include new jars in lib/

10 lines of code changed in 1 file:

• build.xml (+10 -5)

benjamin.redelings 2008-05-03 07:28 Rev.: 842

[FIX] Enable compilation using 'ant'

* build.xml: update lib/* elements
* build_release.xml: ditto.

8 lines of code changed in 2 files:

• build.xml (+7 -2), build_release.xml (+1 -1)

benjamin.redelings 2007-07-23 12:37 Rev.: 421

[FIX] Allow 'ant' to build beast on linux.
* build.xml: add lib/mtj.jar to beast classpath
* build_development.xml: ditto.

95 lines of code changed in 2 files:

• build.xml (+1), build_development.xml (new 94)

benjamin.redelings 2006-11-16 11:05 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)