Fixed indexing issue in the stepping-stone sampling estimator.
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Bugfix for the linear integrator scheme.
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edited TODO
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working on bss UI
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Minor change to text output.
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Generifying IntegratedMixtureModel, so that one can use a mixture of DistributionLikelihood as well.
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working on parser for epoch ancestral state reco
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working on epoch ancestral state reco
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working on epoch ancestral state reco
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general parser
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simplify the parser
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Imported patch attachd to issue 430 - a PearsonCorrelation statistic.
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Cleaned up the tipdate sampling options (the joint prior model wasn't generating code so hid this option). Removed requirement for taxon sets to be at least 2 taxa.
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On second thought, it might just be easier to group several TreeParameterModels together. Committing just to keep a record.
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Cleaning up some of the user-info text on threading.
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Generifying TreeParameterModel to handle multiple data-types (double, double[], int, etc.). Also base abstract class supports an includeTips flag developed in TrialTreeParameterModel (now depricated). NewTreeParameterModel should replace TreeParameterModel after extensive testing.
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Fix for issue with multi-threading not working. The issue was that -threads 0 was being treated as no-multithreading where as it should specify an automatic thread pool size (having no -threads option gives a thread 0 value). For best performance the default should be not to use the thread command line option (but -threads 1 should be used to turn off multithreading). This also affected -beagle_instances as these use the threadpool.
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Fix for http://code.google.com/p/beast-mcmc/issues/detail?id=620 - allows taxon sets of 1 taxon if 'includeStem' is selected.
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Fix for http://code.google.com/p/beast-mcmc/issues/detail?id=623. Logging multiple clock rates to tree logger now gives partition name prefixed tags.
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Fix for http://code.google.com/p/beast-mcmc/issues/detail?id=627 - change in the clock group name now is propagated to the clock table popup.
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Tweaks to hierarchical transmission model
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Added a trait logger for complete histories with times under robust dnds counting
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TreeTransforms are now loggable as branch traits
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AncestralTreeLikelihood does not need a substitution model - it gets it from the site model.
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Fix for issue 611: http://code.google.com/p/beast-mcmc/issues/detail?id=611
Discrete trait rates file now has a proper prefix and is not a hidden file.
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Fix for issue 625: http://code.google.com/p/beast-mcmc/issues/detail?id=625
TreeLikelihood for a non codon-partitioned partition was not being given the correct prefix if there was another codon-partitioned partition.
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Fixed store/restore functionality of BetaDistributionModel
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Very important bug fix - the check boxes in the States panel now line up.
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Starting work on a complete history filter
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Expanding robust counting dNdS to consider complete histories
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Fixed error last revision introduced into TreeParameterModel
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Diplomacy is about surviving until the next century. Politics is about surviving until the next Friday
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Implementing a hierarchical version of the transmission model
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Added a beta distribution model
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Introduced a trial TreeParameterModel that excludes external branches; created a new branch-specific Pagel estimator
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working on parser
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working on parser
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Trying a tree transform
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Refactoring TransformedTree to make generalizations easier
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Hopefully resolves issue 618. Codon-partitioned models do not throw XML errors with ancestral sequence reconstruction. There is still an issue with the "count" parameter name for non-dNdS robust counting. So, non-dNdS robust counting is temporarily disabled for CP models.
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Resolved XML problem with ancestral reconstruction for MRCA that were not the root.
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Correct version of GMRF multilocus likelihood
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Extending allopolyploid model to deal with arbitrary numbers of diploids. Most new code is in new class AlloppDiploidHistory and old class AlloppNetworkNodeSlide.
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epoch model simulation
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epoch model simulation
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parser for beagle simulator
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working on epoch model simulation
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homogenous simulation
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working on beagle simulator
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parser for beagle simulator
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parser for beagle simulator
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working on beagle simulator
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working on beagle simulator
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Fixed AncestralSequenceAnnotator to use KALIGN instead of CLUSTAL (much faster)
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working on BEAGLE seq simulator
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