Changelog • Quartet

VizualizeQuartet() now returns calculation results.
Use spectrum legend in VisualizeQuartet().

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

Fix memory leaks.

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

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

Package ‘vdiffr’ now used conditionally.

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.

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.

Remove deprecated C function ptr_fun.
Clarify some documentation pages.

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.

Improved portability of C++ code.

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

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.