v2.2.0

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.

v2.1.0

• 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().

v2.0.0

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.

v1.16.1

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

v1.16.0

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().

v1.15.0

• 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).
• Modernize aspects of C++ code.

v1.14.0

• 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).

v1.13.1

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

v1.13.0

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

• Add %in% and match methods for phylo / multiPhylo objects.

• Check for overflow in splits functions.

v1.12.0

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.