Release v1.2.3

Changes

• Setting collapseSampledAncestors=true is now ignored -- use fnCollapseSA(tree).
• Temporarily disable FBD-Range models (#449).
• Refactor PhyloOrnsteinUhlenbeckREML (#426)

Features

• Allow mnFile and mnModel to write JSON output if given format="json" (#377)
• Refactor dnBDSTP, dnFBDP, and dnPhylodynamicBDP (#386, #440)
• Compute average distance matrices more efficiently (#454).
• Compute ExponentialError probability densities more efficiently (#432, #434).
• Add member procedure to set node age (#380).
• Add member procedures to remove invariant and gap sites (#379, #392).
• Be less picky about initial tree ages matching ages from taxon files (#455).
• Make mvCollapseExpandFossilBranch complain if r=1 (no fossil sampling) (#440).
• Make power posterior analyses more flexible (#397).

Bug fixes

• Stop BD simulations from hanging in situations with many constraints (#453).
• Stop moving fossil tip nodes in mvRootTimeSlideUniform (#447).
• Fix consensusTree (#441).
• Fix crash reading trees with bad indices (#403, #395).
• Fix ancestral state reconstruction with missing data (#396)
• Fix the uniform topology prior (#442).
• Fix vectorFlatten (#445, #389).
• Fix a memory leak in reversible jump mixtures (#430).
• Fix BDSTP segfault (#367)
• Fix updating phylogenetic likelihood when site mixture probability changes (#437).
• Fix interaction of multiple stopping rules (#458).
• Fix crash with tuning on mvScale (#452).
• Fix writing delimited character data (#362)
• Fix representation of sampled ancestors in tensorphylo functions (#369).
• Fix offset for the read tree trace function (#381).
• Fix Probability(-1) and Probability(2) (#410).
• Don't flatten arrays of stochastic variables in checkpoint files (#448).

Release v1.2.2

Features

• We now use a flag (-j) instead of a separate executable for Jupyter mode.
• Matrices can be added, subtracted, and negated.
• Allow computing SSE likelihoods using TensorPhylo
• Add pipe operator: x |> f(y) now yields f(x,y).
• ... and many bug fixes.

Release v1.2.1

Speed & memory

• Cache transition probability matrices.
• 4x faster tree summaries.
• Discrete character data sets take 5x less RAM, and are 5x faster to load.

Features

• Add Occurence Birth-Death Process.
• Better mixing statistics for MC^3.
• Automatically remove degree-2 root nodes when reading non-clock trees.

Bug Fixes

• Fix some problems with the BDSTP.
• Fix false claim of conflicting constraints. (#250, #288)
• Don't get stuck on MCMC with amino-acid models.
• Fix crash in unrooted NNI and SPR.
• Fix using file paths and directories on Windows.
• Restore dnFBDP synonym for dnBDSTP.
• Restore initialTree argument to dnFBDP .
• Fix check for number of rates in FBD-Range process.
• Fix crash when reading some trees with sampled ancestors. (#240)
• Prevent NumStates methods from overriding character exclusion. (#252)

Release v1.2.0 Lagerstätte

Merge pull request #255 from revbayes/build-singularity-image

Build singularity image & add initial release workflow

RevBayes v1.1.1 A New Hope

Long overdue release with several bug fixes and improvements.

Please see the change log here: https://github.com/revbayes/revbayes/blob/master/NEWS.md

RevBayes v1.1.0 Home Bayes

Quarantine edition.

In December 2019, the repository that used to live here was moved to https://github.com/revbayes/revbayes.archive and a new repository with a flattened history was put in its place.

Version 1.0.13 and earlier are available at https://github.com/revbayes/revbayes.archive/releases