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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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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