April 2007 Commit Log

Number of Commits:

25

Number of Active Developers:

5

sidneym 2007-04-30 02:22 #25 Rev.: 257

shell scripts and cmd files for running BEAST

65 lines of code changed in 10 files:

• bin: beast (+8), beast.cmd (new 5), beauti (+8), beauti.cmd (new 5), loganalyser (+8), loganalyser.cmd (new 5), logcombiner (+8), logocombiner.cmd (new 5), treeannotator (+8), treeannotator.cmd (new 5)

alexei.drummond 2007-04-29 14:25 #24 Rev.: 255

Ported the Bayes factor approximation code from C++ that Marc Suchard shared with me to Java -- lets plug this in to Tracer and automatically calculate the Bayes factor and bootstrap estimated uncertainty for the treeLikelihood statistic... This will facilitate easy model comparison of different substitution models

291 lines of code changed in 4 files:

• src/dr/app/tracer/application: AnalysisMenuFactory.java (+2 -2)
• src/dr/app/util: Arguments.java (+57 -59)
• src/dr/inference/trace: BayesFactor.java (new 231), Trace.java (+1 -4)

jheled 2007-04-25 07:57 #23 Rev.: 251

off by one check results in infinite loop

2 lines of code changed in 1 file:

• src/dr/evomodel/coalescent: CoalescentSimulator.java (+2 -2)

jheled 2007-04-25 07:52 #22 Rev.: 250

Passing just one node into simulateCoalecent results in infinite loop

5 lines of code changed in 1 file:

• src/dr/evolution/coalescent: CoalescentSimulator.java (+5 -2)

rambaut 2007-04-25 03:57 #21 Rev.: 249

Updated the included JEBL library to 0.4. This is required to get BEAUti to compile properly.

9 lines of code changed in 8 files:

• build.xml (+1 -1), build_coalsim.xml (+1 -1), build_development.xml (+1 -1), build_release.xml (+1 -1)
• lib: jebl-0.3.jar (del), jebl-0.4.jar (new)
• src/dr/app/beastdev: BeastVersion.java (new)

rambaut 2007-04-25 03:40 #20 Rev.: 248

Ported improvements and bug fixes from the 1.4.x branch into Trunk.

307 lines of code changed in 13 files:

• src/dr/app/beast: BeastMain.java (+1 -1), BeastVersion.java (+5)
• src/dr/app/beauti: BeastGenerator.java (+20 -4), BeautiApp.java (+7 -3), BeautiFrame.java (+32 -32), BeautiOptions.java (+6 -5), DataPanel.java (+9 -9), PriorsPanel.java (+4 -2), TaxaPanel.java (+193 -77)
• src/dr/app/tools: LogCombiner.java (+5 -5), TreeAnnotator.java (+5 -5)
• src/dr/evolution/util: Taxa.java (+18)
• src/dr/util: Version.java (+2)

rambaut 2007-04-24 23:53 #19 Rev.: 245

Fixed issue 14 (exception if Newick tree not terminated by a ';').

62 lines of code changed in 1 file:

• src/dr/evolution/io: NewickImporter.java (+62 -57)

sidneym 2007-04-24 17:43 #18 Rev.: 243

build script for Windows version of native library

2 lines of code changed in 1 file:

• native: compileNativeWin32.bat (+2)

sidneym 2007-04-24 15:07 #17 Rev.: 241

remove unused local variables that produced compiler warning

0 lines of code changed in 2 files:

• native: NucleotideLikelihoodCore.c (-1)

alexei.drummond 2007-04-24 12:32 #16 Rev.: 240

Added section on running BEAST from the command line

39 lines of code changed in 1 file:

• doc: BEAST14_Manual.tex (+39)

alexei.drummond 2007-04-23 12:39 #15 Rev.: 238

Removed references to example XMLs until we actually have them!

13 lines of code changed in 1 file:

• doc: BEAST14_Manual.tex (+13 -11)

alexei.drummond 2007-04-19 12:21 #14 Rev.: 237

Increased the depth of the table of contents to engineer 42 pages. The manual is now in its first final draft.

1 lines of code changed in 1 file:

• doc: BEAST14_Manual.tex (+1 -1)

alexei.drummond 2007-04-19 12:08 #13 Rev.: 236

Added a table of comments, dealt with Simon's other comments. Fixed up the TreeAnnotator section. General edits.

133 lines of code changed in 1 file:

• doc: BEAST14_Manual.tex (+133 -97)

alexei.drummond 2007-04-19 10:46 #12 Rev.: 235

Simon's edits

142 lines of code changed in 1 file:

• doc: BEAST14_Manual.tex (+142 -127)

alexei.drummond 2007-04-18 18:34 #11 Rev.: 229

Nic's edits debugged...

1 lines of code changed in 1 file:

• doc: BEAST14_Manual.tex (+1 -1)

alexei.drummond 2007-04-18 18:32 #10 Rev.: 228

Nic's edits

123 lines of code changed in 1 file:

• doc: BEAST14_Manual.tex (+123 -96)

alexei.drummond 2007-04-18 18:00 #9 Rev.: 227

damn, I am error-prone today. Copy-paste error. This time it is tested and definitely works. It sure does change the results on my analyses a lot (they look reasonable now!) I wonder how many people have published with this model broken?

7 lines of code changed in 1 file:

• src/dr/inference/operators: DeltaExchangeOperator.java (+7 -1)

alexei.drummond 2007-04-18 17:53 #8 Rev.: 226

oops, forgot to delete one line... now it should work

0 lines of code changed in 1 file:

• src/dr/inference/operators: DeltaExchangeOperator.java (-1)

alexei.drummond 2007-04-18 17:46 #7 Rev.: 225

Added weights to the deltaExchangeOperator
For codon partitions (1+2)+3 you need to add a attribute parameterWeights="2 1" to the deltaExchangeOperator and remove the centredScaleOperator. This should be fixed in BEAUti as well!

36 lines of code changed in 1 file:

• src/dr/inference/operators: DeltaExchangeOperator.java (+36 -10)

alexei.drummond 2007-04-14 14:00 #6 Rev.: 224

Reformatted BEAST14_Manual.tex to have hard wraps. This will allow edits to be smaller, since SVN manages edits on a line-by-line basis.

735 lines of code changed in 4 files:

• doc: BEAST14.tex (+2 -2), BEAST14_Manual.tex (+731 -155)
• src/dr/evomodel/branchratemodel: RateEpochBranchRateModel.java (+1 -1)
• src/dr/math: MersenneTwisterFast.java (+1 -1)

alexei.drummond 2007-04-13 13:15 #5 Rev.: 223

Answered some of Andrew's questions and fixed on error (should use \textit{} instead of \mathit{} when not in math mode ($ $)

10 lines of code changed in 1 file:

• doc: BEAST14_Manual.tex (+10 -15)

rambaut 2007-04-13 12:57 #4 Rev.: 222

added link to jebl library in ant build file

330 lines of code changed in 2 files:

• build_coalsim.xml (+100)
• doc: BEAST14_Manual.tex (+230 -215)

alexei.drummond 2007-04-12 23:08 #3 Rev.: 221

The first draft of a manual for BEAST -- please take a moment to read it and tell me what you think. On Mac OS X a good LaTeX editor is TeXShop 2.1

1070 lines of code changed in 1 file:

• doc: BEAST14_Manual.tex (+1070)

alexei.drummond 2007-04-05 14:52 #2 Rev.: 220

Added the facility to set the temperature of the MCMC chain...

7 lines of code changed in 1 file:

• src/dr/inference/mcmc: MCMC.java (+7)

msuchard 2007-04-03 13:40 #1 Rev.: 219

Added GMRFSkylineLikelihood and GMRFSkylineGibbsOperator classes to begin work on implementing a GMRF smoother on population size trajectories. The classes currently do not do anything.

42 lines of code changed in 2 files:

• src/dr/app/beast: BeastParser.java (+2)
• src/dr/evomodel/speciation: MrBayesDefaultModel.java (+40 -52)

March 2007 »