Release v1.4.1

Speed & memory

• 4-fold speedup in analyses of DNA data when useScaling=TRUE (#1002).

Features

• Add a stop( ) function to halt Rev script execution with a user-specified message (#1019).
• Allow rep( ) to take input of type Probability (#1035).
• Allow specifying a fixed burnin fraction in convergence rules (#1048).

Bug fixes

• DAG
  • Fix a segfault when the model graph contains a cycle (#962).
  • Make sure Model::getOrderedStochasticNodes inserts parents before children (#1050).
• Likelihood evaluation
  • Avoid -inf log likelihoods in fnF81( ) (#1002).
  • Avoid -inf / NaN log likelihoods in mvBetaSimplex (#1002).
• MCMC
  • Draw random numbers regardless of log likelihood difference to reduce test fragility (#1006).
  • Make sure all MPI ranks finished writing to a trace file before convergence rules read it (#1029).
  • Require the frequency argument of convergence rules to be strictly positive (#1044).
  • Make it simpler to exclude vector variables from mnModel (#1052).
• Interface
  • Do not print asterisks ad infinitum when running .burnin( ) for zero generations (#1049).
  • Make sure help pages show the constructors, arguments, and domain types for all overloads of a given distribution (#1056).
• Misc
  • Make sure mnStochasticVariable and Mcmc::checkpoint write out the hidden state (allocation index) of dnMixture (#987).
  • Fix reading of RNA datasets (#1018).
  • Fix handling of extant samples when rho=0 and of purely extinct trees in dnBDSTP (#1032).
  • Make sure the .getStateDescriptions( ) method preserves the first-seen state order (#1036).
  • Prevent dnPhyloWhiteNoise from taking the log of an already log-transformed density (#1054).
  • Fix initialization issues with backbone-constrained nonclock analyses (#1056).
  • Fix handling of parameter-specific timelines in dnBDSTP (#1059).

Refactor

• Refactor partial likelihood scaling (#1002).
• Remove pointer arithmetic (#1026).

Documentation improvements

• Expand documentation for srGelmanRubin, srGeweke, srMinESS, srStationarity (#1048).

Infrastructure

• Enable and improve support for the AVX instruction set (#1002).
• Add support for building and developing RevBayes using the Nix package manager (#1033).

New contributors

• @sriram98v made their first contribution in #1033.
• @wnsplim made their first contribution in #1050.

Release v1.4.0

Backwards-incompatible changes

• Remove the tuneTarget argument from those moves that are not capable of being tuned (#947).
• Remove dnPhyloCTMCDollo (#997).
• Temporarily disable the uniform partitioning distribution (dnUPP) (#999).

Speed & memory

• Slight speedup in analyses employing dnPhyloCTMC when useScaling=TRUE (#816).
• Much faster merging of log files with mcmc(..., combine="mixed") (#981).

New models/analyses

• Model selection via leave-one-out cross-validation (#460).
• StairwayPlot method for inferring demographic histories from site frequency spectra (#460).
• State-dependent Brownian motion (BM) and Ornstein-Uhlenbeck (OU) processes (#904).

Features

• Add functions for folding site frequency spectra and creating StairwayPlot vectors (#460).
• Add function for reading stochastic character maps (#904).
• Allow vector input to ln( ) and log( ) (#948).
• Add an .isRooted( ) method to Tree (#952).
• Add -p flag to print commands from -e expression or script (#978).
• Make stochastic mapping and ancestral state monitors work for all types of discrete characters (#994).

Bug fixes

• Tree handling
  • Fix handling of quoted labels and tree-level comments when reading Newick trees (#799).
  • Treat unrooted trees as such when generating summaries (#932).
  • Fix parsing of nested comments in Newick trees (#946).
  • Make sure the mrcaIndex( ) function and .unroot( ) method work on rooted nonclock trees (#952).
  • Refactor the .reroot( ) method of Tree objects (#966).
• Moves
  • Fixes to mvRateAgeProposal and mvRateAgeSubtreeProposal (#908, #940).
  • Make sure the tuneTarget argument is honored when present (#947).
• Checkpointing
  • Prevent checkpoint file corruption by partial overwrites (#935).
  • Prevent duplicated iterations when resuming from a checkpoint (#970).
  • Add serialization support to MatrixReal for checkpoint use (#983).
• Crash / NaN
  • Fix a segfault in the help2yml executable built with MPI (#937).
• Misc
  • Fix issues with missing values in multisample BM and OU processes (#905).
  • Fix handling of the burnin argument in posterior predictive simulations (#923).
  • Correct reasoning about return types for max( ), median( ), min( ), sum( ) (#938).
  • Check for mismatches in the number of states between an SSE model and underlying data (#974).
  • Make sure writeNexus( ) keeps all state labels when concatenating character matrices (#975, #995).
  • Make sure we start the interactive loop when -i is given even if there is an error (#977).
• Non-user-facing
  • Clean up partial likelihood caching in dnPhyloCTMC (#816).
  • Switch from C++17 to C++23, supporting those features that are available in GCC 12 (#927).
  • Add assertion checks to Tree::getNode( ) (#972).
  • Fix hidden virtual functions (#976, #984).
  • Fix various compiler warnings (#998).

Documentation improvements

• ConditionalPosteriorOrdinate, dnStairwayPlot, fnBSPInterval, fnFoldSFS, mvAdaptiveRJSwitch, mvRandomCategoryWalk (#460).
• Expand documentation for dnMultinomial, mvRandomGeometricWalk, mvRandomIntegerWalk, mvRandomNaturalWalk (#460).
• CharacterHistory, dnPhyloBrownianProcessStateDependent, dnPhyloCTMCDASiteIID, dnPhyloOrnsteinUhlenbeckStateDependent, mvCharacterHistory, readCharacterHistory (#904).
• mrcaIndex (#952).

Infrastructure

• Fix continuous-integration (CI) tests on macOS where boost 1.90 is broken (#924).
• Update build.sh for setting boost location with modern CMake (#925).
• Make sure the CI test script fails when tutorial tests fail (#940).
• Allow tests that require TensorPhylo (#941).
• Make sure the CMake build script does not drop extra arguments if -boost_root is given (#951).
• Fix compile cache misses (#959).
• Help database cleanup (#989).
• Make meson always build the help2yml executable (#990).

New contributors

• @HaoqingDu made their first contribution in #905.

Release refs/tags/debug-EBD-build2

Compiled binaries to provide extra information for issue #955

Release v1.3.2

Backwards-incompatible changes

• Restructure the command-line interface following Rscript syntax (#803, #827).
• Change the name of the first argument of TraceTree.getUniqueTrees( ) from credibleTreeSetSize to minCladeProbability (#819).
• Change the name of the first argument of TraceTree.isTreeCovered( ) from ci_size to credibleTreeSetSize (#819).
• Remove the argument num_taxa from TraceTree.computeEntropy( ) (#819).
• Remove mvAddRemoveTip (#862).

Features

• Allow executing Rev expressions from the command line (#803).
• Allow handling partial ambiguities involving a gap state (#838).
• Add function for writing alignments to Phylip format (#882).
• Add arguments to dnPhyloCTMC to account for observational error (#901).

Bug fixes

• Summary trees
  • Prevent .reroot( ) from incorrectly reassigning node and branch annotations (#804).
  • Report 95% HPD intervals for the ages of sampled ancestors (#810).
  • Fix majority-rule consensus trees with sampled ancestors (#859).
• MCMC
  • Do not print confusing messages about tip age adjustments on initialization (#821).
  • Allow specifying tuningInterval = 0 in mcmc.burnin( ) (#843) and powerPosterior.burnin( ) (#878).
  • Make sure mnModel extracts the right nodes from the model graph (#900).
• Moves
  • Safely undo node time moves if there are no nodes for them to operate on (#829).
  • Make sure tip time moves use the right node index in each MCMC run (#895).
• Crash / NaN
  • Fix the block bootstrap when the number of samples is small (#842).
  • Fix a segfault in FBD analyses with multiple parameter-specific timelines (#861).
• Misc
  • Multiple fixes for TraceTree methods (#819).
  • Fix FBD analyses with a single parameter-specific timeline (#845).
  • Allow subscripting arrays by any variable that can be typecast to Natural (#856).
  • Fix printing Simplex objects in validation analyses (#876).
  • Fix the ODE solver used in dnCDBDP and dnTVSSE (#883).
  • Remove null terminators from .methods( ) output (#886).
  • Ensure compiler-independent output in complex FBD analyses (#895).
  • Fix dnPhyloBrownian (#897).
  • Fix dnGeometric (#907, #915).

Documentation improvements

• Expand documentation for mvSlice (#614).
• Expand documentation for TraceTree (#819).
• args (#830, #851).
• dnPhyloCTMC
  • Add a description of the coding argument (#832).
  • Expand the provided example to show how to simulate characters (#868).
  • Formatting fixes (#867, #871).
  • Add a description of the new observationErrorProbability and observationErrorFrequencies arguments (#901).
• mvFNPR (#839).
• Minor fixes to write (#852) and dnBeta (#900).
• Corrections to srGeweke and multispecies coalescent distributions (#871).
• Add a description of the burninMethod argument of convergence rules (#871).
• Miscellaneous formatting fixes (#871).

Infrastructure

• Do not require the system boost library in CMakeLists.txt (#831).
• Increase the minimum CMake version from 3.5 to 3.10.2 (#834).
• Sync the Nexus Class Library (NCL) with the upstream repo (#837)
• GitHub Actions updates (#841, #892).
• Update meson build instructions (#857).
• Remove a duplicated test file to suppress a git clone warning (#873).

New contributors

• @mcranium made their first contribution in #839.
• @curiosusJR made their first contribution in #873.

Release v1.3.1

Backwards-incompatible changes

• Change the distribution name of the sampled-speciation birth-death model from dnSBBDP to dnSSBDP (#714).

Features

• Distributions
  • Add a topologically constrained distribution for the state-dependent speciation and extinction process (#693).
  • Allow nonzero rho values in FBD analyses without extant tips (#788).
  • Make dnGLHBDSP faster and allow reporting stochastic mappings (#693).
• Methods / arguments
  • Add an .nbranches( ) method to Tree (#759).
  • Add a method for calculating the standard error of marginal likelihood estimates (#779).
  • Add a nanoseconds option to time( ) (#796).
• Interface
  • Nicer printing of member method lists (#800).
• Misc
  • Biogeography: allow regional features and non-existent regions (#693).

Bug fixes

• Regression fixes
  • Fix posterior predictive simulations that were broken in 1.3.0 (#778).
  • Fix validation analyses that were broken in 1.3.0 (#814).
• Member procedures
  • Fix .getTopologyFrequency( ) behavior for tree traces (#750).
  • Fix .resolveMultifurcations( ) behavior in edge cases (#771, #780).
• Nexus I/O
  • Make sure writeNexus( ) can handle BranchLengthTree vectors (#758).
  • Fix parsing of the STATELABELS block in Nexus files (#760).
  • Allow reading Nexus files with an ASSUMPTIONS block (#764).
• MPI / MC^3
  • Fix segfault in MPI + MC^3 (#763).
  • Fix logging and progress monitoring for .runOneStone( ) + MPI (#782).
• Moves
  • Fix argument name mismatch in mvUpDownSlide (#766).
  • Fix mvEllipticalSliceSamplingSimple to not require strict equality of likelihoods (#773).
  • Reject tree moves if there are no nodes for them to operate on (#798, #802).
• Misc
  • Synchronize dirty flagging for nodes and transition probability matrices (#773).
  • Fix caching to avoid crashes when using dnReversibleJumpMixture (#773).
• Partial
  • Avoid subscripting by -1 in dnAutocorrelatedEvent (#773).

Documentation improvements

• Basic data types: Integer, Natural, Probability, Real (#714).
• Birth-death models: dnCBDSP, dnCDBDP, dnSSBDP (#714).
• Marginal likelihood estimators: pathSampler, steppingStoneSampler (#779).
• Expand documentation for TraceTree (#800).

Infrastructure

• Update DLLs to allow running RevStudio on Windows (#751).
• Don't print operator summaries in coalescent tests, and only run 1 generation (#770).
• Enable testing with assertions to detect out-of-bounds indices in std::vector (#773).
• Don't skip remaining scripts in a test if one fails, and combine error message from multiple failing scripts in a test (#773).
• Allow specifying a required exit code to allow/require failure (#773).
• Fix check for missing output files (#773).
• Make test runner output clearer and more informative (#773).
• Replace boost::filesystem with std::filesystem (#807).

New contributors

• @prilau made their first contribution in #796.

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 v1.2.4

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.