Changes in version 1.4.0                        

  - QuartetConsensus() finds the tree minimising summed symmetric
    quartet distance to a set of trees (Takazawa et al. 2026).
  - PairwiseQuartets() compares quartet statuses between all pairs of
    trees.
  - TripletDistance() is now an S3 generic accepting phylo, multiPhylo,
    list, and file-path (character) inputs (previously file-paths only).
  - TripletDistance(), PairsTripletDistance(), and
    AllPairsTripletDistance() now use the CPDT algorithm of Jansson &
    Rajaby (2017) instead of the tqDist file-based backend, giving a
    ~100× speedup for triplet-distance calculations.
  - Quartet distances no longer abort with "Leaves don't agree" when a
    tree has a unifurcating root; the bundled tqDist tree reader treated
    the redundant root as a spurious extra leaf (#64).
  - Require R 3.6, dropping dependency on viridisLite.

                 Changes in version 1.3.0 (2026-03-19)                  

  - New QuartetConsensus() finds the tree minimizing the sum of
    symmetric quartet distances to a set of input trees (Takazawa et
    al. 2026), using a greedy add-and-prune heuristic.
  - OpenMP parallelism for quartet calculations.
  - Improvements to memory allocation and cache performance.
  - Move ResolvedQuartets() core computation to C++.
  - Reduce inefficient R-side processing in
    SingleTreeQuartetAgreement(), QuartetStatus() and
    TwoListQuartetAgreement().
  - R <4.1 is no longer formally supported.

                 Changes in version 1.2.7 (2024-10-31)                  

  - VizualizeQuartet() now returns calculation results.
  - Use spectrum legend in VisualizeQuartet().
  - Include CSL file within package to remove external dependency.

                 Changes in version 1.2.6 (2024-02-09)                  

  - Drop obsolete C++11 specification.
  - Update minimum R version to 3.5 (for Ternary).
  - R <3.6 is no longer formally supported.

                 Changes in version 1.2.5 (2022-07-08)                  

  - Fix memory leaks.

                 Changes in version 1.2.4 (2022-05-02)                  

  - QuartetStates() handles absent leaves gracefully.
  - Copy-edit documentation.

                        Changes in version 1.2.3                        

  - Replace deprecated function TreeTools::in.Splits().
  - Update test cases in readiness for TreeTools v1.7.0.

                 Changes in version 1.2.2 (2020-12-09)                  

  - Package 'vdiffr' now used conditionally.

                 Changes in version 1.2.0 (2020-10-21)                  

New features

  - CompareQuartetsMulti() compares quartet status in one tree with
    status in multiple others.
  - VisualizeQuartets() depicts contribution of splits to quartet score.
  - SimilarityToReference() allows comparison against specified
    reference topology.

Changes

  - Deprecate RobinsonFoulds(): renamed to RawSymmetricDifference().
  - QuartetState[s]() now uses sister-of-4 notation, rather than
    sister-of-1, to give values within [0, 3].
  - ManyToManyQuartetAgreement() now returns entries for N and Q.

Improvements

  - Faster C++ implementation of AllQuartets() and QuartetStates().
  - QuartetStatus() now supports non-identical leaf samples.
  - SimilarityMetrics() now handles single tree comparisons.
  - Correctly calculate resolution of unrooted trees with unconventional
    node numbering conventions.
  - Remove errant name when comparing unnamed tree pairs.
  - Small improvements to PlotQuartet().
  - Minor efficiency improvements.
  - Documentation improvements.

                 Changes in version 1.1.0 (2020-01-28)                  

  - Pass trees directly to C, without writing to temporary intermediate
    file.
  - Use TreeTools in place of TreeSearch, supporting new Splits class.
  - Facilitate comparison between lists of multiple trees.
  - Fix Latex error in vignettes.

                 Changes in version 1.0.3 (2019-12-30)                  

  - Remove deprecated C function ptr_fun.
  - Clarify some documentation pages.

                 Changes in version 1.0.2 (2019-03-06)                  

  - Force R 3.5.0-style random number generation in examples, to ensure
    backward compatibility.
  - Add caterpillar trees to sq_trees, to illustrate issues with
    partition-based distance metrics.

                 Changes in version 1.0.1 (2019-01-22)                  

  - Improved portability of C++ code.

                 Changes in version 1.0.0 (2019-01-16)                  

New features

  - Add functions to generate ternary plots from tree similarity
    measures.

Improvements

  - Use tqDist for all quartet calculations.
  - Remove single "splits" from splits objects.
  - Simplify installation via github_install.
  - Add missing details to documentation.

Modifications

  - Function SimilarityMetrics now takes the output of
    QuartetStatus(trees), rather than a list of trees.
  - Function SplitStatus now returns output using the same column
    headers as QuartetStatus
  - Column N added to QuartetStatus output.
  - Function names changed, to become more precise:
      - QuartetMetrics → SimilarityMetrics
      - MatchingSplits → SplitStatus
      - MatchingQuartets → QuartetStatus
      - Choices → AllQuartets

                        Changes in version 0.2.0                        

Modifications

  - Add MatchingSplits function to calculate number of splits
    contradicted / unresolved.
  - Add vignettes to document when the quartet metric may be preferable
    to other tree distance metrics.