NEWS.md

In Quartet: Comparison of Phylogenetic Trees Using Quartet and Split Measures

Quartet v1.2.5

• Fix memory leaks.

Quartet v1.2.4

• 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

• Package 'vdiffr' now used conditionally.

Quartet v1.2.0

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

• 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

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

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.

Quartet documentation built on July 8, 2022, 5:08 p.m.