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.

v1.11.1

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