v2.5.0

• New functions to measure cluster sizes (see ?"cluster-statistics").

• KMeansPP() conducts clustering using K-means++, replacing K-means in app.

• New vignette on tree landscape analysis.

v2.4.1

• New vignette on how to compare tree sets.

• PathVector() now treats trees with a root node as rooted.

• Fix plot layout in treespace vignette.

• Informative failure when not enough memory for consensus_info().

• Replace throw with stop in C++.

v2.4.0

• 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.

v2.3.0

• Support ConsensusInfo(p > 0.5).

• Address hypervolume comparison in vignettes.

• Support uniform manifold approximation and projection in app.

v2.2.0

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

• Support for parallel computation via StartParallel().

• Progress bars.

v2.1.1

• Solaris compatibility.

• Modest vignette improvements.

• spic/scic abbreviation recognition.

v2.1.0

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.

Renamed functions

• Project()/ProjectionQuality() re-named to MapTrees()/MappingQuality().
• SpectralClustering() re-named to SpectralEigens().

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.

v2.0.3

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

v2.0.2

• Diagnose and fix memory leaks

• Explicitly import shiny/shinyjs functions

v2.0.0

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

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

• 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.