Directory examples/treePriors/

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dong.w.xie 2010-08-26 16:13 Rev.: 3452

Trunk: refactory xml examples

0 lines of code changed in 14 files:

• examples/treePriors: testBSP.xml (del), testBirthDeath.xml (del), testBirthDeathAsYule.xml (del), testBirthDeathPrior.xml (del), testCataclysmCoalescent.xml (del), testCoalescent.xml (del), testGMRFCoalescent.xml (del), testLinearBSP.xml (del), testPiecewiseExponential.xml (del), testYule.xml (del), testYuleCase3.xml (del), testYuleModel.xml (del), testYuleModel_10taxa.xml (del), testYulePrior.xml (del)

msuchard 2010-07-13 23:31 Rev.: 3305

Keeping example file up-to-date

6 lines of code changed in 2 files:

• examples/treePriors: testGMRFCoalescent.xml (new)

alexei.drummond 2010-05-10 15:35 Rev.: 3163

test case for Yule with one "reference" calibration

0 lines of code changed in 1 file:

• examples/treePriors: testYuleCase3.xml (new)

dong.w.xie 2009-12-10 13:34 Rev.: 2675

Trunk: start merge from branch 1.5 in

8 lines of code changed in 2 files:

• examples/treePriors: testCataclysmCoalescent.xml (+8 -6)

alexei.drummond 2009-07-15 16:25 Rev.: 1860

refactoring to remove illegal dependencies (dr.inference should not depend on dr.evo*.*) and tidying

109 lines of code changed in 1 file:

• examples/treePriors: testYuleModel_10taxa.xml (new 109)

alexei.drummond 2009-07-05 19:18 Rev.: 1823

tidying up some of the example files -- the eventual aim is for the tag names for id/idref pairs to always match for consistency, and enhanced ability to use standard parsing tools such as XMLSchema et cetera. At the moment I have modified XMLParser so that it just prints a warning to stderr unless strictXML is turned on, in which case an XMLParserException is thrown when the tag names of an id/idref pair don't match.

16 lines of code changed in 6 files:

• examples/treePriors: testCoalescent.xml (new), testYuleModel.xml (new), testYulePrior.xml (+2 -2)

alexei.drummond 2009-05-14 15:51 Rev.: 1714

update coalescent test - was failing to run tree log analysis

8 lines of code changed in 1 file:

• examples/treePriors: testCoalescent.xml (+8 -6)

rambaut 2009-03-25 04:40 Rev.: 1513

Added an alternative parameterization of PiecewiseExponential that has a vector of pop sizes and a final ancestral growth rate. This should help with mixing (having a vector of growth rates was problematic because of the interaction between adjacent rates).

14 lines of code changed in 2 files:

• examples/treePriors: testPiecewiseExponential.xml (+14 -1)

rambaut 2008-11-20 13:03 Rev.: 1321

Added a piecewise-exponential growth model.

358 lines of code changed in 1 file:

• examples/treePriors: testPiecewiseExponential.xml (+358)

alexei.drummond 2008-08-23 02:27 Rev.: 1168

refactoring of ALS stuff with Alex

8 lines of code changed in 2 files:

• examples/treePriors: testYule.xml (+8 -8)

alexei.drummond 2008-08-06 06:39 Rev.: 1085

testCataclysm and some unit test examples of how to test BEAST MCMC without any XML!

209 lines of code changed in 1 file:

• examples/treePriors: testCataclysmCoalescent.xml (+209)

alexei.drummond 2008-07-22 03:50 Rev.: 999

tidying

1 lines of code changed in 1 file:

• examples/treePriors: testYuleModel.xml (+1 -7)

alexei.drummond 2008-05-12 09:37 Rev.: 863

updated yule tests. Removed old birth death models

312 lines of code changed in 3 files:

• examples/treePriors: testBirthDeathAsYule.xml (new 298), testYuleModel.xml (+3 -3), testYulePrior.xml (+11 -4)

alexei.drummond 2008-05-12 09:04 Rev.: 856

updated to log trees in nexus

6 lines of code changed in 1 file:

• examples/treePriors: testYuleModel.xml (+6 -4)

msuchard 2007-08-21 08:38 Rev.: 522

1 lines of code changed in 1 file:

• examples/treePriors: testGMRFCoalescent.xml (+1 -1)

msuchard 2007-08-14 12:59 Rev.: 499

Started Gibbs operator for fixed effects in the GMRF

551 lines of code changed in 1 file:

• examples/treePriors: testGMRFCoalescent.xml (+551 -168)

bloomquist 2007-08-14 09:28 Rev.: 498

Temporary commit for Marc. Working on GMRF block update class.

167 lines of code changed in 1 file:

• examples/treePriors: testGMRFCoalescent.xml (+167 -51)

alexei.drummond 2007-08-11 22:35 Rev.: 491

still working on genrea dna covarion model -- the parameters seem to be in the wrong cells of the matrix...

358 lines of code changed in 1 file:

• examples/treePriors: testLinearBSP.xml (new 358)

alexei.drummond 2007-08-11 21:18 Rev.: 490

organizing examples folder

1685 lines of code changed in 8 files:

• examples/treePriors: testBSP.xml (new 357), testBirthDeath.xml (new 221), testBirthDeathPrior.xml (new 201), testCoalescent.xml (+172), testGMRFCoalescent.xml (+125), testYule.xml (+215), testYuleModel.xml (+110), testYulePrior.xml (+284)