Quartet v1.2.2 2020-12-09

  • Package ‘vdiffr’ now used conditionally.

Quartet v1.2.0 2020-10-21

New features

Changes

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 2020-01-28

  • 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 v1.0.3 2019-12-30

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

Quartet v1.0.2 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 v1.0.1 2019-01-22

  • Improved portability of C++ code.

Quartet v1.0.0 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:
    • QuartetMetricsSimilarityMetrics
    • MatchingSplitsSplitStatus
    • MatchingQuartetsQuartetStatus
    • ChoicesAllQuartets

SlowQuartet v0.2.0 Unreleased

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.