NEWS

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Quartet 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.

Quartet 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.

Quartet 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.

Quartet 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.

Quartet 1.2.5 (2022-07-08)

• Fix memory leaks.

Quartet 1.2.4 (2022-05-02)

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

Quartet 1.2.3

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

Quartet 1.2.2 (2020-12-09)

• Package 'vdiffr' now used conditionally.

Quartet 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.

Quartet 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.

Quartet 1.0.3 (2019-12-30)

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

Quartet 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.

Quartet 1.0.1 (2019-01-22)

• Improved portability of C++ code.

Quartet 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

Quartet 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.