Add '-heights ca' option to set heights which do not suffer from the "negative branches" problem. citation later ....
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XML generating
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working on XML generation
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Grammar
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Fixed calculation of intervalLikelihood to properly use intervalWidth (rather than assuming 1.0).
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Remove truncation and make likelihood in terms of titre H_ij rather than immunological distance d_ij
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Standardizing output for markov jumps
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Improving ease to subclass ComplexSubstitutionModel for varying conditioning restrictions
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Increased max iterations and largest allowable condition number for complex diagonalizable substitution models; may change inference in BSSVS models.
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changed to take a user-specified matrix
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SubstitutionModelDelegate returns the root substitution model's frequencies.
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Added warning about single-child internal nodes that is suppressed in TreeStat but active in BEAST-MCMC and other programs.
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Added SingleChildCountStatistic to TreeStat to support e.g. the counting of direct ancestors and nodes representing migration events.
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Standardizing format for complete histories with single events
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Relaxed nexus importer to allow internal nodes with 1 or more children. This is to allow TreeStat to analyze direct ancestor trees and migration trees where migrations events are defined by internal nodes.
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Modified NexusImporter to handle nested arrays. May cause unforeseen bugs in important other traits.
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Preliminary test unit for failure of eigen decompositions
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Consistently clearing complete histories within CodonPartitionedRobustCounting
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Small correction in keeping track of the number of steps.
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Delegated handling of missing values in IntegratedMultivariateTraitLikelihood with a view towards enabling partially missing values
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ARGAddRemoveEventOperator updated to handle two partitions
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Fixed bug in PrecisionMatrixGibbsOperator under power posterior
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Added transition kernel for disjoint geographic regions
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A better solution to the multithreading issue with trees that avoids thread syncs. The problem was only for empirical trees for which the branch lengths were known but not the node heights. Thus it had to compute the node heights when asked and this caused the thread conflict. Now the EmpiricalTrees object forces a node height calculation prior to evaluation.
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There was an issue when multiple BTL tried to get node heights from the same tree in different threads giving negative branch length errors. Synchronizing on the tree fixes this - might have other implications.
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Updated PrecisionMatrixGibbsOperator for functionality within path sampling from posterior to prior. Should still cause errors in path sampling between two arbitrary models.
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Extra level of indirection to stay off NoClassDefinition errors for MPI
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Another small tip date-related modification.
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Removed the canReturnComplexDiagonalization() method which was always returning false even if there was a complex diagonalization. This method is correctly returned by the substitution model.
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Removing a debug exit()
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Fixed bug in SubstitutionModelDelegate; new and old BeagleTreeLikelihood now return same values.
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Added MPI ranking of output for embarrassingly parallel use on Keeneland.
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