• Package ‘vdiffr’ now used conditionally.

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.
  • 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:
    • QuartetMetricsSimilarityMetrics
    • MatchingSplitsSplitStatus
    • MatchingQuartetsQuartetStatus
    • ChoicesAllQuartets

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.