Changes in version 2.4.0.9000                      

Bug fixes

  - Consensus(trees, p) now retains a split present in exactly a
    proportion p of trees (i.e. in ceiling(p * length(trees)) trees) for
    p > 0.5, matching the documentation and ape::consensus(); previously
    such a split was dropped at exact thresholds (e.g. a split in 2 of 3
    trees with p = 2/3). The majority threshold p = 0.5 is unchanged (a
    split must occur in more than half the trees).

Performance

  - Guarantee preorder return from root_on_node() to simplify
    Consensus() internal pre-processing
  - Consensus() and SplitFrequency() defer materialising a split's bit
    pattern until it is needed, so splits that never reach the consensus
    threshold are no longer built. Identical results; up to ~13× faster
    for large trees (greatest gains for tall trees / many tips), with no
    change at small sizes.
  - RenumberTips() relabels an unlabelled multiPhylo or list of trees in
    a single C++ pass instead of a per-tree R loop, with a no-op fast
    path for trees already in the target order. Speeds up Consensus()
    and other callers when combining many trees; results are unchanged.
  - Consensus() no longer copies every input tree to strip branch
    lengths and node labels (the consensus core ignores both); it now
    coerces in place, trimming wrapper overhead (~25% faster on small
    forests of many short trees). Results are unchanged.

                 Changes in version 2.4.0 (2026-06-02)                  

New features

  - RandomTree(), YuleTree(), PectinateTree(), BalancedTree(),
    StarTree(), and SingleTaxonTree() allow lengths to accept a function
    that generates edge lengths (e.g. RandomTree(8, lengths = runif)).
  - PaintTree() assigns colours to every edge, leaf, and internal node
    such that sister clades occupy adjacent hue bands proportional to
    their tip counts, with saturation growing from zero at the root to
    one at every tip.
  - NexusTokensToInteger() converts character data to integers, mapping
    uncertain tokens to NA.
  - ReadTntCharacters() attaches an xgroup attribute (factor) when a TNT
    xgroup partition block is present.

Performance

  - Consensus() computes majority-rule and threshold consensus trees in
    time linear in the number of trees (previously quadratic), after
    Jansson, Shen & Sung (2016); implementation informed by their FACT
    package. SplitFrequency() inherits the same single-pass speed-up.

Fixes

  - NexusTokens() once again handles polymorphism tokens with internal
    whitespace (e.g. (1 2), {0 1}).

                 Changes in version 2.3.0 (2026-04-23)                  

Bug fixes

  - ReadTntCharacters() now handles multi-line comments, bare &
    continuations, @taxonomy suffixes, name-only taxon lines, mid-line
    xread, smart-quote names (Windows-1252), and packed multi-taxon
    lines.

Performance

  - Drop stringi dependency.
  - as.character.Splits() re-implemented in C++; ~3× faster on 200-tip
    trees.

Usability

  - Consensus() and SplitFrequency() now respond to user interrupts
    during long-running computations.
  - SL_MAX_TIPS compile-time constant increased to 32704, allowing
    support for larger trees.

                 Changes in version 2.2.0 (2026-03-20)                  

New functionality

  - EdgeRatio() reports the ratio of external:internal edges.
  - SplitInformation() supports Splits and phylo objects.
  - sort and order support Splits objects.
  - SplitFrequency(reference = NULL) returns frequency of all splits.
  - as.TreeNumber() now supports trees with up to 51 leaves
    (previously 19). Trees with 20–51 leaves have more than 2^64
    distinct topologies, so their TreeNumber is stored as a decimal
    character string rather than integer64. The 19-leaf limit for
    integer64-backed storage (and as.MixedBase() round-trips) is
    unchanged.
  - as.TreeNumber() no longer warns for trees with 20–44 leaves.
  - inst/include/TreeTools/tree_number.h added to support downstream
    packages (e.g. TBRDist) via LinkingTo: TreeTools. Provides 256-bit
    tree number encoding/decoding supporting up to 51 leaves, extended
    from the 44-leaf limit of the previous uint64_t-based
    implementation.

Performance

  - SplitFrequency(reference = NULL): split normalization moved to C++;
    internal split de-duplication uses hash map instead of ordered map.
  - NodeDepth() for unrooted trees rewritten as O(n) two-pass C++
    algorithm, replacing iterative R while-loop.
  - duplicated.Splits() uses hash-based O(n) de-duplication, replacing
    O(n²) pairwise comparison.
  - RenumberTips.multiPhylo() applies tip permutation in a single C++
    call, avoiding per-tree overhead.

Fixes

  - PhyDatToMatrix() no longer crashes on zero-character phyDat objects
    (e.g. from a star tree); returns a 0-column matrix with correct row
    names.
  - AddUnconstrained() handles zero-character phyDat input gracefully.

Dependencies

  - RCurl moved from Imports to Suggests; ReadMrBayesTrees() uses
    RCurl::url.exists() when available, falling back to base R url() for
    URL checks.

                 Changes in version 2.1.0 (2026-02-11)                  

  - Add method RenumberTips.Splits().
  - FirstMatchingSplit(x) provides performant alternative to
    match(x)[[1]].
  - Support logical pole in PolarizeSplits().
  - RenumberTree() supports numeric tipOrder input.
  - Support larger trees in ClusterTable objects.
      - Retires CT_PUSH and CT_POP macros.
  - Support larger trees in Consensus().
      - Uses 32-bit integers, necessitating downstream changes to
        TreeDist.
  - Remove hard limit on tree size in SplitList.
  - MatrixToPhyDat() gains tipLabels parameter.
  - Document return value for J1Index().

                 Changes in version 2.0.0 (2025-09-23)                  

New functionality

  - Cherries() counts the cherries in a binary tree.
  - New method as.Splits.integer().
  - Add methods for NULL objects.

Fixes and enhancements

  - Fix RoguePlot(sort = TRUE) (Rogue#33).
  - Remove R.cache dependency: UnrootedKeys() now uses a native cache
    implementation.

Backward incompatible changes

  - Require R 3.6.
  - Remove deprecated functions AllDescendantEdges(),
    .EnforceOutgroup(), ForestSplits(), in.Splits(), PhylogeneticInfo(),
    SpectrumLegend(), SplitNumber(), TreeSplits().
  - Remove deprecated C++ macro TREETOOLS_SPLITLIST_INIT.

                 Changes in version 1.16.1 (2025-08-24)                 

  - Compiler-safe vector initialization, resolving M1-SAN warnings.

                 Changes in version 1.16.0 (2025-08-22)                 

New functionality

  - SplitConsistent() calculates split (dis)agreement.
  - LongBranch() identifies long-branched taxa.
  - Treeness() computes the treeness (=stemminess) of a tree, a proxy
    for its phylogenetic signal.
  - Add KeepTip() methods to correspond to DropTip().
  - Preorder() gains topologyOnly argument.

Enhancements

  - MakeTreeBinary() explicitly removes edge lengths.
  - Optimize ClusterTable class.
  - Optimize NSplits().
  - Remove exported C++ cache objects to prefer calculation with
    intrinsics.
  - Other performance improvements.

Fixes

  - Fix as.ClusterTable() when leaf order varies.
  - Fix regressions in as.ClusterTable() that caused downstream errors.
  - Fix regressions in PhyToString().
  - Fix handling of multiple ambiguities in Reweight().

                 Changes in version 1.15.0 (2025-07-21)                 

  - Reweight() sets the weight of characters in a phylogenetic dataset.
  - MatchStrings() checks for mismatched tip labels, suggesting
    corrections.
  - RootTree() gains fallback argument to handle outgroups that do not
    root a tree.
  - Fix MakeTreeBinary() labelling trees as in preorder.
  - Fix as.Splits.matrix(tipLabels != NULL).
  - Improve performance of PhyToString().
  - Modernize aspects of C++ code.

                 Changes in version 1.14.0 (2025-05-13)                 

  - AddTip(lengthBelow = NA) adds leaf at node without adding a new
    edge.

  - BalancedTree() and equivalent gain a lengths parameter to specify
    edge lengths.

  - Fix taxa misplaced by RoguePlot(sort = TRUE).

  - Fix unexpected polytomies in Consensus() (#168).

                 Changes in version 1.13.1 (2025-04-07)                 

  - Support non-unique labels in DropTip() checks.

                 Changes in version 1.13.0 (2025-01-10)                 

  - %in% and match methods for phylo / multiPhylo objects.

  - Decompose() decomposes additive (ordered) phylogenetic characters by
    binary decomposition.

  - Check for overflow in splits functions.

                 Changes in version 1.12.0 (2024-07-25)                 

New methods and functions

  - TopologyOnly() removes metadata from phylo objects.
  - J1Index() computes the robust, universal tree balance measure of
    Lemant et al. 2022 doi:10.1093/sysbio/syac027, incorporating code by
    Rob Noble.

Enhancements

  - Consistent sequence of list entries in phylo objects.
  - RandomTree() returns trees for < 3 leaves.
  - root_on_node() handles trees with < 2 leaves.
  - Support larger trees in TotalCopheneticIndex(), fixing #158.

                 Changes in version 1.11.1 (2024-06-07)                 

  - Set random seed and increase tolerance to avoid false negatives on
    tests.

                 Changes in version 1.11.0 (2024-06-05)                 

New methods and functions

  - YuleTree() generates a random tree by the Yule process.
  - DescendantTips() complements DescendantEdges(), rewritten in C++,
    fixing a bug when edges were not in preorder.
  - NodeNumbers() returns the indices of nodes within a tree.

Enhancements

  - RandomTree(root = TRUE) roots the tree on a random edge.
  - RoguePlot()$legendLabels returns suggested labels for legend.
  - Support node labels in AddTip(), CollapseNode(), DropTip(),
    MakeTreeBinary(), Renumber(), Reorder(), SortTree(), Subtree()
    (#149).
  - AddTip(edgeLength = NULL) defaults to lengthBelow. This will become
    the default in a future release.
  - An entry point to the C++ function root_on_node() is now exported
    (intended for expert use only).
  - Fix handling of weighted trees by root_on_node().
  - Use KeepTip() internally so SplitFrequency() supports Splits objects
    as documented.

                 Changes in version 1.10.0 (2023-08-18)                 

New methods and functions

  - TipTimedTree() displays trees where leaves are associated with
    absolute ages.
  - ReadMrBayesTrees() samples trees from posterior of MrBayes output.
  - is.TreeNumber() method.

Improvements

  - Support zero-edge trees in as.Splits() and NSplits().
  - Support empty constraints in AddUnconstrained().
  - Add space between tokens in WriteTntCharacters() to support
    continuous characters (#139).

Deprecations and breaking changes

  - Change order of parameters in DescendantEdges()
  - Deprecate AllDescendantEdges(); use DescendantEdges() instead.
  - Deprecate EnforceOutgroup(); use RootTree() instead.
  - Remove NonDuplicateRoot() and in.Splits().

                 Changes in version 1.9.2 (2023-04-27)                  

  - Improve support for comments in ReadNotes().
  - Support Nexus-escaped ''s in ReadCharacters().
  - Add legend parameter to RoguePlot().
  - RoguePlot() now returns invisibly.
  - Deprecate SpectrumLegend() -- spun off to separate "PlotTools"
    package.

                 Changes in version 1.9.1 (2023-03-20)                  

  - AddUnconstrained() and ImposeConstraint() handle wider range of
    inputs.

  - PhyDatToMatrix() can (and by default does) override levels to write
    ambiguous tokens in custom formats such as {01}.

  - Call C functions using symbols, not strings.

                 Changes in version 1.9.0 (2022-11-28)                  

New methods and functions

  - ZeroTaxonTree() creates a phylo object with no leaves.

  - DropTip() gains new methods DropTip.list() and DropTip.NULL().

  - as.matrix.phylo() converts a tree to a matrix representation,
    allowing a tree to be passed as a constraint to ImposeConstraint().

  - as.matrix.Splits() and as.matrix.phyDat() methods added as synonyms
    to as.logical.Splits() and PhyDatToMatrix().

Improvements

  - Handle TipLabels(0) and BalancedTree(0).

  - Support zero-leaf trees in as.Splits() and duplicated.Splits().

  - Support non-identical tip labels in as.Splits().

  - Try Latin-1 encoding if ReadCharacters() family fail under UTF-8.

                 Changes in version 1.8.0 (2022-09-15)                  

New methods and functions

  - TntOrder() renumbers a tree's nodes to match TNT's convention.

  - head() and tail() methods for Splits objects.

  - Set names of splits object with names(splits) <- ....

  - as.Splits() support character vectors in the form "...***".

Improvements

  - ReadTntTree() reads tree tags and follows TNT node numbering
    conventions.

  - SpectrumLegend() gains title parameter and more styling options.

  - Support > 32767 trees in Consensus() (#127).

  - DropTip() speed improved when branch lengths are present.

                 Changes in version 1.7.3 (2022-07-20)                  

  - ReadTntTree() supports multi-line trees.

  - as.MixedBase() supports larger trees (44-32767 tips).

  - Add deprecation warning to in.Splits().

                 Changes in version 1.7.2 (2022-05-24)                  

  - RenumberTips() drops "preorder" attribute, as reordering tip labels
    may break edge ordering guarantee.

  - Native implementation of ClusterTable class.

  - Replace throw with stop in C++ scripts.

                 Changes in version 1.7.1 (2022-03-25)                  

  - AddTip(): Fix bug when adding tip to root of weighted tree.

                 Changes in version 1.7.0 (2022-03-21)                  

New methods and functions

  - rev.Splits() reverses order in which splits are listed.

  - KeepTip.Splits() is a faster alternative to SubSplit().

  - %in%.Splits() retains names when comparing small splits (#40).

  - sort.multiPhylo() sorts lists of trees according to their mixed base
    representation (#84).

  - Bitwise manipulation of splits with |, &, xor.

  - as.MixedBase() uniquely represents binary trees as a mixed-base
    vector.

  - PathLengths() describes all paths within a tree.

  - KeptVerts() and KeptPaths() identify elements in reduced trees.

  - PostorderOrder() describes a sequence of edges corresponding to a
    postorder traversal of a tree.

  - SpectrumLegend() adds gradients to plot legends.

Improvements

  - Improve handling of zero-split trees.

  - DropTip() no longer adds a root to unrooted trees, and retains edge
    lengths.

  - Improve speed of DropTip(), by an order of magnitude in some cases.

  - Support edge lengths in Preorder(), RootTree(), UnrootTree() and
    Postorder() (#49, #89).

  - Fix bug when tree is rooted on a discontinuous outgroup.

  - SortTree() handles weighted and non-binary trees (#25, #25), and
    gains option to sort by tip labels.

  - TipsInSplits(smallest = TRUE) counts tips in smaller bipartition.

  - Fix a bug with phyDat objects in ArtificialExtinction().

  - RenumberTips() allows tipOrder to contain elements not present in
    tree.

  - Use lighter Rcpp headers.

  - Small improvements to computational efficiency.

Deprecations

  - Remove deprecated function PostorderEdges() (#35).

                 Changes in version 1.6.0 (2022-01-12)                  

New functions

  - RoguePlot() plots the positions of rogue taxa.

Improvements

  - DropTip() gains check parameter to allow slightly faster operation
    where input is guaranteed to be valid.

  - RandomTree() gains nodes parameter allow the inclusion of
    polytomies.

  - Infer tips parameter if missing in StringToPhyDat().

  - Remove dependency on "phangorn" (allowing use on R < 4.1)

  - Improve parsing of information from nexus files.

  - Export DropTipPhylo() as wrapper to DropTip.phylo().

                 Changes in version 1.5.1 (2021-10-06)                  

  - PhyDatToMatrix() optionally encodes ambiguous / inapplicable tokens
    as NA.

  - Implement sort.multiPhylo().

  - Update test suite for compatibility with "testthat" > 3.0.4
    (@hadley, #83).

                 Changes in version 1.5.0 (2021-09-08)                  

New functions

  - ConstrainedNJ() returns an approximation to a neighbour-joining tree
    that respects constraints.

  - PolarizeSplits() marks a specified taxon as representing the ingroup
    of all splits.

  - Add KeepTip() and improve performance of DropTip().

  - ImposeConstraint() makes a tree consistent with topological
    constraints.

  - as.phylo.Splits() represents a Splits object as a tree.

  - Consensus() is a faster C++ implementation of ape::consensus().

  - ClusterTable() C++ functionality imported from "TreeDist".

Improved functions

  - Warn when empty cells passed to MatrixToPhyDat().

  - Warn when LabelSplits(labels) lack names.

  - SplitFrequency() drops tips from forest that aren't in reference.

  - AddTipEverywhere() supports trees with < 3 leaves.

  - Make RootTree() and PhyDatToMatrix() more robust.

  - Support encoding option in ReadCharacters() function family.

  - Support CHARSTATELABELS in ReadCharacters().

  - Support for more formatting quirks in ReadNotes().

  - Better support ambiguous tokens in WriteTntCharacters().

Optimization

  - Fast matching functions from "fastmatch".

  - Improve efficiency of Preorder() and Postorder(), and lift limit on
    tree size.

                 Changes in version 1.4.5 (2021-06-23)                  

  - Correct calculation of minimum value in TCIContext().
  - Extract tip labels from objects in StringToPhyDat().
  - Support AddTip(tree, where = "tip name").
  - SplitFrequency() supports four-leaf trees.
  - Add RootTree.matrix() method for edge matrices.
  - Add TipLabels.phyDat() method.
  - Add NULL methods for tree reordering functions.
  - Additions and improvements to text parsing functions.

                 Changes in version 1.4.4 (2021-04-20)                  

  - Add NTip.phyDat() method.
  - Update MakeTreeBinary() docs and tests to reflect updated behaviour
    of ape::multi2di() in 'ape' v5.5.

                 Changes in version 1.4.3 (2021-04-12)                  

  - AddTip() supports edge lengths.
  - CladisticInfo() supports Splits objects.
  - as.multiPhylo() converts trees, datasets and Splits objects into
    multiPhylo objects.
  - LabelSplits(labels = NULL) labels each split with its associated
    node.
  - PhyDatToMatrix() supports integer-only levels.
  - SortTree() supports lists of trees.
  - Improvements to ReadTntCharacters() character block extraction
    (#50).

                 Changes in version 1.4.2 (2021-01-26)                  

  - Support star trees in RootTree().
  - Improve memory handling in root_on_node().
  - Documentation linkage.

                 Changes in version 1.4.1 (2020-12-09)                  

  - MSTEdges() supports distance matrices with > 256 entries.
  - Package 'vdiffr' used conditionally.

                 Changes in version 1.4.0 (2020-10-19)                  

New functions

  - MSTLength() reports length of minimum spanning tree.
  - AllTipLabels() returns all labels from all trees in a list.
  - PairwiseDistances() (from 'TreeDistData') computes distances between
    all pairs of trees in a list.
  - ArtificialExtinction() gains replaceAll option.
  - WriteTntCharacters(types = ...) writes different character types to
    TNT file.
  - Tree characterization S3 methods: add .default and .NULL.

Enhancements

  - MSTEdges() implemented in C++, improving runtime by orders of
    magnitude.
  - Improved parsing of TNT character files.

                 Changes in version 1.3.1 (2020-10-03)                  

  - Improved parsing of TNT files.
  - Fix misspecified C++ linkage.

                 Changes in version 1.3.0 (2020-09-22)                  

New functions

  - SisterSize() and RootNodeDist() measure sister-clade size and
    root-node distance.
  - MSTEdges(): Edges of minimum spanning tree.
  - SplitImbalance(): how balanced is each split?
  - New C++ functions root_on_node() and root_binary() to root trees
    quickly and robustly.

Enhancements

  - TNTReadTree() handles additional punctuation characters.

  - Import RdMacros package 'Rdpack'.

  - C++ implementation of TipsInSplits().

  - Export C++ functions preorder_edges_and_nodes() and
    postorder_edges().

  - Remove obsolete copy of C++ code from 'phangorn'.

                 Changes in version 1.2.0 (2020-08-03)                  

  - ArtificialExtinction(): Remove characters that are absent in a
    fossil template.
  - WriteTntCharacters(): Write morphological dataset in TNT format.
  - Improve TNT dataset parsing.
  - Documentation improvements.

                 Changes in version 1.1.0 (2020-07-07)                  

New functions

  - RandomTree(): Draw tree from uniform distribution, instead of via
    ape::rtree().
  - MakeTreeBinary(): Uniform equivalent of ape::multi2di().
  - match.list() method for lists of splits.
  - SplitsInBinaryTree(): How many splits occur in an n-leaf binary
    tree?
  - vapply64(), sapply64(), replicate64(): helper functions when a
    function returns a 64-bit integer.

Enhancements

  - Use methods for UnrootTree(), RootTree(), RootOnNode() to support
    lists of trees.

                 Changes in version 1.0.0 (2020-06-08)                  

New functions

  - CladisticInfo(): Calculate the information content of a tree.
  - RootNode(): Which node is a tree's root?
  - UnrootTree(): Safely remove a root node.
  - NodeDepth(): Discriminate shallow from deep nodes.
  - NodeOrder(), NDescendants(): Count edges incident to each node.
  - CladeSizes(): Count leaves / nodes descended from each node.
  - ListAncestors(): List ancestors of a node.
  - LabelSplits(): Label splits on plotted tree.
  - DropTip(): Remove tip, handling weird node orders.
  - LeafLabelInterchange(): Exchange position of n tips.
  - StarTree(): Generate unresolved tree.
  - TotalCopheneticIndex() integrated from 'tci' package.

Deprecations

  - PostorderEdges(): use Postorder() instead.
  - NonDuplicateRoot(): unused internal function.
  - match.Splits(): use match() instead.
  - in.Splits(): use %in%.Splits() instead.

Enhancements

  - Improve support for unrooted trees in as.Splits().
  - Use methods so Reorder functions can handle multiPhylo objects and
    edges.
  - Handle funny node orders.
  - Support continuous characters in ReadCharacters().
  - Improve performance of as.logical.Splits() and related functions.
  - Fail nicely when trees are too large for memory.
  - Fix memory leak in as.Splits().
  - Various under-the-hood improvements to functions.
  - Documentation improvements.

                 Changes in version 0.1.4 (2020-03-04)                  

  - Catch hang-inducing bugs in RootOnNode().
  - Update doubleFactorials cache to fix as.integer() rounding error.
  - Support unrooted trees in AddTipEverywhere().
  - Documentation improvements.

                 Changes in version 0.1.3 (2019-12-19)                  

  - RootOnNode(): Quickly root a tree on a specified node.
  - Improve portability of C++ code.

                 Changes in version 0.1.2 (2019-12-18)                  

  - as.Newick: Fast conversion to Newick format.
  - as.TreeNumber: Tree shape enumeration.

                        Changes in version 0.1.1                        

  - Add functions to translate trees to mixed base integers.
  - RenumberTips can extract tip order from phylo and Splits objects.
  - Documentation changes to satisfy CRAN submission requirements.

                        Changes in version 0.1.0                        

  - Pre-release version spun out of 'TreeSearch' package. Some
    functionality is subject to change.