• New vignette on how to compare tree sets.
  • Fix plot layout in treespace vignette
  • Informative failure when not enough memory for consensus_info().
  • Replace throw with stop in C++.
  • Correct calculation of trustworthiness and continuity metrics.

  • Depict strain in minimum spanning trees with StrainCol() and helper function MSTSegments().

  • Update tests for consistency with “TreeTools” v1.7.

  • Use lighter Rcpp headers.

  • Support ConsensusInfo(p > 0.5).

  • Address hypervolume comparison in vignettes.

  • Support uniform manifold approximation and projection in app.

  • Speed improvements, using optimizations suggested by Alexis Stamatakis’ Bioinformatics group.

  • Support for parallel computation via StartParallel().

  • Progress bars.

  • Solaris compatibility.

  • Modest vignette improvements.

  • spic/scic abbreviation recognition.

New features

  • ConsensusInfo() quickly calculates the splitwise information content of the consensus of a set of trees, after Smith (forthcoming).

  • SplitwiseInfo() and ClusteringInfo() gain a p parameter to reflect the reduced information content of splits with lower support values, and a sum parameter to allow return of individual split information content.

  • KCDiameter() approximates the diameter of the Kendall-Colijn metric.

  • Plot3() (experimental) provides pseudo-3D plotting.

Improvements

  • Add self-organizing map example to treespace vignette.

  • Allow the specification of custom vectors in the Kendall–Colijn metric.

  • Faster all-to-all tree distance calculation.

  • Diagnose and fix memory leaks, including over-long reported matchings.

  • Explicitly import shiny/shinyjs functions.

  • Project() launches ‘shiny’ app for projection and analysis of tree space.

  • ProjectionQuality() calculates trustworthiness and continuity of tree space mappings.

  • Faster calculation of Robinson–Foulds distance (using algorithm of Day (1985)) and clustering information distance.

  • New class ClusterTable to allow faster distance computation with Day (1985) algorithm.

  • Improve error messages in CalculateTreeDist().

  • Improvements to vignettes.

  • Use package ‘vdiffr’ conditionally.

  • Import RdMacros package ‘RdPack’.
  • TreeDistance() and related functions now return a dist object when computing all distances between all pairs of trees in a list.

  • Improve floating-point arithmetic in TreeDistance() functions.

  • TreeDistance() now returns a distance (as documented), rather than a similarity.

  • Fix rounding error in NNI ‘Li’ upper estimate, and improve NNI performance.

  • Reduce precision of LAPJV so rounding errors do not result in interminable run times.

  • Fix range errors when calculating tree distances.
  • Initial release, building on some draft functions included in ‘TreeSearch’ 0.3.2.9005.