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Quartet v1.2.7 (2024-10-31)

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

Quartet v1.2.6 (2024-02-08)

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

Quartet v1.2.5 (2022-07-08)

  • Fix memory leaks.

Quartet v1.2.4 (2022-05-02)

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

Quartet v1.2.3

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

Quartet v1.2.2 (2020-12-09)

  • Package 'vdiffr' now used conditionally.

Quartet v1.2.0 (2020-10-22)

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 v1.1.0 (2020-01-29)

  • 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 v1.0.3

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

Quartet v1.0.2

  • 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 v1.0.1

  • Improved portability of C++ code.

Quartet v1.0.0 (2019-01-09)

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

SlowQuartet v0.2.0 (2017-11-22)

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.