Backwards compatibility so MarkovJumps XML blocks do not crash BEAST without BEAGLE.
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A _very_ situation specific simulator for a project.
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Classes for modelling the relative rates of loci.
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TRUNK: *BEAST mapping file example
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TRUNK: change build
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Updating geo-spatial regions for Gibbs sampling
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Special tolerance test for super-high precision Colt eigendecomposition
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Fixed Issue 331 <http://code.google.com/p/beast-mcmc/issues/detail?id=331>. I removed the help button until such time as it does something. I have added some tooltip text for the various buttons. This should be done for all UI in BEAUti. I also changed the two toolbars into a single one at the top of the panel so they didn't affect the rescaling of the splitpane.
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Fixed Issue 336 <http://code.google.com/p/beast-mcmc/issues/detail?id=336>. The SubstModel table in Site Model Tab now has a minimum width.
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Fixed Issue 339 <http://code.google.com/p/beast-mcmc/issues/detail?id=339>. This involves not installing the scroll pane as the rootPane of the frame if on the Mac OS X platform. For this platform it also sets a minumum window size of 800x600. At this size, some of the UI gets clipped in some panels but my goal now is to improve the UI to prevent this rather than forcing the user to scroll the panel. I will leave it up to developers on other platforms to decide whether to follow this pattern or to allow scrollable UIs.
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Prevent repetitive rate calculations.
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328 lines of code changed in 3 files:
Automatically create bounds for the category parameter and correction to adding parameter to model.
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Correction of typos.
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TRUNK: fix breaken code in test, but wait Alexei to verify the test.
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fixed tests (by removing! yikes!)
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removed unmappable character
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TRUNK: correct dev parser name
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updated Birth-death serial sampling model
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TRUNK: a simple solution for Issue 321: Default priors in BEAUTi still lead to IMPROPER posterior
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TRUNK: solve Issue 319: BEAUti: checkbox 'allow different taxa in partitions' should be a message instead
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Special tolerance test for super-high precision Colt eigendecomposition
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Forgot a couple of other things...
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Minor fix for debugging
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Cleaned up the GeneralSubstitutionModel parser even more. This involved getting rid of SVSIrreversibleSubstModel (old code, Marc promises me). RootFreqs are gone - only worked with the old Irreversible model. Can be done other ways now. svsComplexSubstitutionModel and svsGeneralSubstitutionModel are synonyms of this parser and should allow backwards compatibility.
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Add ability to select a random subset of taxa for analysis
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Parser and corrections for DiscretizedLociRates.
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Models the relative loci rates using the given discritized parametric distribution.
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Cleaned up GeneralSubstitutionModelParser so it generally uses SVSGeneralSubstitutionModel or SVSIrreversibleSubstitutionModel (creating indicators = 1 if not specified). The only case now where it will use GeneralSubstitutionModel is if relativeTo attribute is specified.
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adding the ability to consider unions of polygons in GeoSpatialCollection
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adding the ability to consider unions of polygons in GeoSpatialDistribution
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TRUNK: remove beagle-beast.jar from release to include beagle in beast jar.
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TRUNK: *BEAST mapping file - Gopher data example
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TRUNK: fix *BEAST GUI bug to load mapping file
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TreeAnnotator requires classes recently moved into dr/app/gui; fixed
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Bifractional diffusion is a pain
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JUnitTest for empirical Bayes smoother
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Mighty cool positive selection tools through simple nucleotide models.
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TRUNK: another bug fix for *BEAST generator
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TRUNK: fix *BEAST GUI bug
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Cleaning up dN/dS summary statistics and adding TreeTraits for flu backbone
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BEAST-BEAGLE JUnits (require BEAGLE, can disable on Hudson if necessary).
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Add several wrappers to convert automatically between different reductions of TreeTraits (sum over tree, sum across sites, etc.). One can even double-wrap to get sum over tree + sum across sites. This should reduce substantial code-duplication and earn me a gold star.
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Started work on multilocus GMRF Skyride
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Keeping example file up-to-date
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Pacifying Hudson.
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Can independently specify root distribution from CTMC stationary distribution
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Checking normalization of CTMC likelihood over all possible alignments
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Branch rate models can now return a logDensity so that they may include the correct normalization constants.
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TRUNK: solve Issue 325: processValues[] in DiscreteTraitBranchRateModel should be the size of number of states NOT number of rates
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Fix with traitName in SampledMultivariateTraitLikelihood
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Gibbs sampling for a single msat ancestral state.
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