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