Release v1.3.0

Backwards-incompatible changes

• Change the name of the tuning argument of mvUpDownSlide from lambda to delta.
• Change the name of the first argument of Tree.reroot( ) from clade to outgroup.
• In powerPosterior( ), specifying cats=N sets up N analyses numbered 1--N, rather than N+1 analyses numbered 0--N.

Features

• Interface
  • Print convergence statistics during MCMC runs with stopping rules if verbose=2 (#645, #657, #739).
  • Better progress monitoring for power posterior analyses (#673).
• Methods / arguments
  • Add member procedure for randomly resolving multifurcations (#641).
  • Add an nruns argument to readTrace( ) (#736).
• Functions
  • Add function for minimum branch length time-scaling (#641).
  • Add trigonometric functions (#647, #648).

Bug fixes

• Checkpointing
  • Fix segfault when attempting to resume an MPI analysis (#646).
  • Fix mismatch of chain states and chain heats when resuming an MC^3 analysis (#670).
  • Don't skip iterations when logging a resumed MC^3 analysis (#727).
• MPI / MC^3
  • Fix NaN heats in MC^3 (#661).
  • Make sure MPI runs the specified number of independent replicates (#662).
• Model graph
  • Only convert deterministic nodes to constant nodes if they really are constant (#678).
  • Fix crash in user functions (#687).
  • Make sure indexing by a deterministic variable creates a deterministic node (#719).
  • Only type-convert variables based on value if they are constant (#721).
• Moves
  • Fix mvRateAgeBetaShift (#688).
  • Allow moves to propose out-of-range indices (#709).
  • Allow moves with low probability ratio and high Jacobian/Hastings ratio (#728).
• Member procedures
  • Fix .dropTip( ) behavior for multifurcations (#640).
  • Fix .getStateDescriptions( ) behavior when subsetting by state space (#696).
  • Fix .reroot( ) behavior when specifying an outgroup by its name string (#742).
• Misc
  • Fix stochastic character mapping when there are excluded characters (#636).
  • Fix handling of large integers on Windows (#708).
  • Don't ignore negative clade constraints (#711).
  • Allow for machine uncertainty in dnEpisodicBirthDeath with empirical sampling (#713).
  • Fix partial likelihood caching in dnPhyloCTMC (#729).
  • Allow reading multiple trees from a string (readTrees(text = ...)) (#735).
• Partial
  • Prevent some instances of clamped values from being modified (#600).

Documentation improvements

• Simplex (#606).
• Moves
  • mvBetaSimplex, mvDirichletSimplex, mvElementSwapSimplex (#606).
  • mvDPPValueBetaSimplex, mvDPPValueScaling, mvDPPValueSliding (#666).
  • mvNNI, mvSPR, mvScale, mvScaleBactrian, mvSlide, mvSlideBactrian, mvTreeScale, mvUpDownScale, mvUpDownSlide (#683)
• sin (#648, #683).
• Substitution models
  • fnJC (#649).
  • fnF81, fnGTR, fnHKY, fnK80, fnK81, fnT92, fnTrN (#653, #656).
  • fnLG, fnWAG (#655).
  • fnFreeK (#667).
  • fnCovarion (#704).
  • fnFreeBinary (#706).
• exp (#653).
• Complete and standardize documentation for dnBernoulli, dnBeta, dnBimodalLognormal, dnBimodalNormal, dnBinomial, dnCategorical, dnCauchy, dnChisq, dnDirichlet, dnExponential, dnGamma (#663).
• dnUniformInteger, fnReadVCF, vectorFlatten (#667).
• Expand documentation for powerPosterior (#673).
• matrix, var (#681).
• floor, mnModel, reverse, sinh (#683).
• power, write (#690).
• Analysis output types and I/O functions
  • readTrace (#702, #723, #736).
  • readTreeTrace (#703, #722, #723, #736).
  • Trace, TraceTree (#723).
• Discretization functions: fnDiscretizeDistribution, fnDiscretizeGamma (#707).

Infrastructure

• Update validation tests (#473).
• Fix continuous-integration builds by dropping openlibm (#644).
• Change build files to streamline updates to the help database (#659).
• Make tutorial tests more flexible (#674).
• Make sure the test runner can handle tutorial checkpoint tests (#676).
• Add integration tests for revised coalescent classes (#689).
• Change website submodule to pull from source rather than master (#692).

New contributors

• @sigibrock made their first contribution in #648.
• @raymondcast18 made their first contribution in #649.
• @PhyloevoTi made their first contribution in #655.
• @ixchelgzlzr made their first contribution in #703.
• @basanta33 made their first contribution in #704.
• @Levi-Raskin made their first contribution in #711.

Release v1.2.5

Backwards-incompatible changes

• Remove underPrior argument to mcmc.run( ) and mcmcmc.run( ). You can use model.ignoreAllData() instead.
• Remove dnLogexponential. You can use dnExponential(l) |> tnLog() instead.
• Remove tree.makeBifurcating() in favor of tree.suppressOutdegreeOneNodes(). To resolve a trifurcation
  at the root you can use reroot(..., makeBifurcating=TRUE) instead.
• The collapseSampledAncestors=true/false setting was removed because it no longer has an effect. If you see a warning Unknown user setting with key 'collapseSampledAncestors' when starting rb, remove the corresponding line in the file .RevBayes.ini in your home directory.

Features

• Allow fossil age sampling with an initial tree in dnConstrainedTopology (#481).
• Transformed distributions:
  • Add shift/scale/exp/log/logit/invlogit-transformed distributions (e.g. dnExp(1) |> tnShift(2)). (#466, #500)
  • Allow C + dist, C - dist, dist - C, and C*dist for a constant C and distribution dist. (#617)
• Allow ignoring data from specific nodes with e.g. model.ignoreData(seqData,morphData,...) (#628)
• Extend type( ) to optionally show the full type-spec (#504).

Bug fixes

• Multiple fixes for building, especially on Windows (#490, #491, #493, #494, #495, #496, #498).
• Checkpointing
  • Fix FBD checkpointing bugs related to dnBDSTP (#484) and fossil time moves (#502, #517).
  • Fix MC^3 checkpointing bug (#553).
• Types
  • Fix type conversion to integer so that it employs deterministic nodes (#545).
  • Make RealPos coherent between conversion and construction (#554).
  • Make vectorFlatten work on more type (#514).
• Crash / NaN
  • Fix dnMixture of rate matrices and other Cloneable objects (#501).
  • Fix treeAssembly sometimes failing to initialize branch lengths (#509).
  • Fix crash if a file changes while we are source( )-ing it (#510).
  • Fix segfault with dnConstrainedTopology + dnUniformTimeTree (#513).
  • Fix a segfault in Model::getOrderedStochasticNodes (#569).
• MCMC: initialization
  • Fix fossil age sampling with an initial tree in dnBDSTP (#480).
  • Fix FBD initialization issues (#537, #561).
  • Extend the starting tree simulator to account for origin/root age (#561).
• MCMC
  • Fix recalculation of likelihoods for Brownian motion distributions (#596).
  • Fix recalculation of likelihoods with mvRootTimeSlideUniform (#594).
  • Fix recalculation of likelihood with treeAssembly (#549).
  • Fix Gelman-Rubin (PSRF) and stationarity stopping rules (#555).
  • Don't move fossil tips outside their age ranges (#559).
  • Fix operator summary for MC^3 when moves are tuned (#522).
• Debug:
  • Log reason for -Inf and NaN probabilities (#592).
  • Add options debugMCMC and logMCMC for investigating likelihood recalculation bugs (#570, #575, #593).
  • More informative error message in treeAssembly when number of branch lengths is wrong (#605).
• Misc
  • Allow reading non-square matrices (#564).
  • Allow checking args.size() when no arguments are given. (#479).
  • Balance braces when printing Matrix (#615).

Documentation improvements

• dnPhyloCTMC( ) (#487).
• fnDiscretizeBeta( ) (#625).
• model( ) (#538).
• time( ) (#572, #574)
• --setOption / setOption() / getOption() (#583)
• Clarify differences between .clamp() and .setValue() (#599).
• Stopping and convergence rules (#488).
• mcmc and mcmcmc
  • .run( ) (#485, #488).
  • .initializeFromCheckpoint( ) (#505).
  • moveschedule parameter and the weight parameter of moves (#506).
• Corrections to dnBivariatePoisson (#539) and mcmcmc (#541).

Release v1.2.5-beta1

This is a test release. If people could check that this works with their analyses, that would be great.

What's Changed

• Merge development into master by @bredelings in #461
• Release 1.2.4 by @bredelings in #476
• Ensure that we can check args.size() even when no arguments are given. by @bredelings in #479
• Fix issue #354 once again by @davidcerny in #480
• Detail the mcmc.run method by @ms609 in #485
• Update dnPhyloCTMC.md by @ms609 in #487
• Sampling fossil ages with dnConstrainedTopology + initial tree by @davidcerny in #481
• Missing S in Boost_INCLUDE_DIRS by @ms609 in #491
• Restarting FBD trees properly from checkpoint by @bjoelle in #484
• Single call to target_link_libraries by @ms609 in #496
• Big object support by @ms609 in #495
• Add build/ to .gitignore by @ms609 in #490
• multiple rules generate ../rb.exe by @ms609 in #493
• Boost_INCLUDE_DIRS by @ms609 in #498
• Stopping rules by @ms609 in #488
• Allow constructing log-scaled distributions directly by @bredelings in #466
• Fix branch length NaN by @bredelings in #509
• Modify type( ) so that you can see the full type-spec by @bredelings in #504
• Avoid crashing if a file changes while we are source( )-ing it. by @bredelings in #510
• Eliminating the WithOffset distributions by @davidcerny in #503
• Policies relevant to Boost by @ms609 in #494
• Distributions for transformed random variables by @bredelings in #500
• Prevent segfault with dnConstrainedTopology + dnUniformTimeTree by @davidcerny in #513
• Fixing broken checkpointing in FossilTipTimeSlideUniformProposal by @bjoelle in #502
• Fix mixture distribution. by @bredelings in #501
• Document mcmc.initializeFromCheckpoint() by @ms609 in #505
• How the weight parameter is used in move proposals by @ms609 in #506
• Generic vector flatten by @bredelings in #514
• Correct operatorSummary for MC^3 when moves are tuned by @davidcerny in #522
• Updated package version in Windows automated actions by @bjoelle in #527
• Another checkpointing fix for FossilTipTimeSlideUniformProposal by @davidcerny in #517
• Fix #532 by @davidcerny in #537
• Doc model by @bredelings in #538
• Fix dnBivariatePoisson documentation by @davidcerny in #539
• Documentation corrections by @ms609 in #541
• Type conversion fix by @bjoelle in #545
• Making RealPos type coherent between conversion and construction by @bjoelle in #554
• Check some invariants for AbstractPhyloCTMCSiteHomogeneous by @bredelings in #550
• MCMCMC checkpointing fix by @bjoelle in #553
• Change starting tree simulator to account for origin/root age by @bjoelle in #561
• Stop tree rescaling from changing ages of SAs or their direct parent by @bjoelle in #559
• Fix Gelman-Rubin and stationarity stopping rules by @davidcerny in #555
• dnInverse by @ms609 in #562
• Allow reading non-square matrices by @davidcerny in #564
• fixing a segfault in Model::getOrderedStochasticNodes by @mikeryanmay in #569
• Convert some MCMC checks from #ifdef to options. by @bredelings in #570
• Document time by @ms609 in #572
• Another time() doc fix by @davidcerny in #574
• Debug mcmc by @bredelings in #575
• Bump xcode 14→15 by @ms609 in #588
• Mark overridden functions by @ms609 in #589
• Some virtual functions are never overridden. Make them non-virtual. by @bredelings in #591
• Remove useless exceptions by @bredelings in #590
• Fix mvRootNodeTimeSlideUniform by @bredelings in #594
• Log reason for -Inf and NaN by @bredelings in #592
• Improve MCMC checks by @bredelings in #593
• Get rid of sprintf in favor of snprintf by @davidcerny in #595
• Document runtime options by @davidcerny in #583
• Fix problems with brownian motion distributions. by @bredelings in #596
• Document mvSlice by @ms609 in #568
• Correctly resetting the branch lengths via treeAssembly after the corresponding moves being rejected by @jsigao in #549
• Distinguish .clamp() and .setValue() by @ms609 in #599
• Report values in error message by @ms609 in #605
• Make stdout and stderr accessible to the test runner by @davidcerny in #604
• Use stream format for RbException by @ms609 in #611
• Try unbreaking macOS ARM tests. by @bredelings in #616
• Integration test for MC^3 by @davidcerny in #612
• Balance braces in print(MatrixReal() by @ms609 in #615
• Don't reject Metropolis-Hastings proposals because one PDF changes from NaN or Zero to something positive and finite. by @bredelings in #613
• Change the makeBifurcating() method by @davidcerny in #618

Full Changelog: v1.2.4...v1.2.5-beta1

Release v1.2.4

Features

• Refactor coalescent to allow heterochronous samples and more.
• Allow constructing substitution models as SiteMixtureModel objects.
• Imputation of missing entries in AverageDistanceMatrix

Bug fixes

• Fix simulation of rate categories with variable coding.
• Fix operator[] in AverageDistanceMatrix

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