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RevBayes 1.2.3 (Apr 26, 2024)

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).

RevBayes 1.2.2 (Jun 7, 2023)

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.

RevBayes 1.2.1 "Peitenimi" (Nov 7, 2022)

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)
  • C++ standard switched to C++17.

RevBayes 1.2.0 "Lagerstätte" (Aug 3, 2022)

New MCMC moves

  • slice sampling (mvSlice) can now do geometric scaling.

New models/analyses

  • New codon models:
    • Goldman-Yang (1994), Muse-Gaut (1994), FMutSel (Yang 2008)
    • Create of Codon models using stackable blocks fndNdS, fnX3, fnMutSel, fnMutSelAA
    • i.e. fnMutSel( fndNdS( fnX3( fnGTR(er, pi), omega ), F ) # GTR + X3 + dNdS + MutSel
  • New dinucleotide models: fnX2, fnMutSel
    • i.e. fnMutSel( fnX2( fnHKY(kappa, nuc_pi) ), F ) # HKY + X2 + MutSel
  • New birth death models:
    • Birth death sampling treatment process (Magee et al. 2020)
    • Time-heterogeneous fossilized birth death range process

New features

  • optional weighting in fnAverageDistanceMatrix
  • FBD range model uses individual fossil occurrence data
  • site mixture allocations work with codon models
  • automatic handling of whitespace delimited files

Bug fixes

  • fixed occasional crashes when using recovering a tree from a checkpoint file due to rounding. Checkpointing now records doubles without rounding
  • fixed a bug when printing individual elements of average distance matrices and calculating their completeness

RevBayes 1.1.1

Changes

  • Warning: this version includes changes to the Random Number Generator, meaning analysis output will be different from v1.1.0, even when run with the same seed.

New models/analyses

  • new PoMo rate matrices with selection

Bug fixes

  • fixed an error in the likelihood calculation for discrete characters when using ambiguous characters and partitioning standard data by state number
  • fixed a bug causing unbounded likelihoods when using PhyloBrownianProcessREML with unrooted trees
  • fixed a crash when using ordered rate matrices
  • fixed a crash when printing the value of a rate matrix
  • fixed a crash when using nested clade constraints
  • fixed a crash when using DEC models
  • fixed an issue with using simplex indexes in deterministic nodes
  • fixed a bug allowing NodeTimeSlideUniform to move sampled ancestor nodes