TreeDist 2.2.0.9000 (development) Unreleased

  • Discussion of hypervolumes in vignettes.

TreeDist 2.2.0 2021-09-13

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

  • Support for parallel computation via StartParallel().

  • Progress bars.

TreeDist 2.1.1 2021-07-13

  • Solaris compatibility.

  • Modest vignette improvements.

  • spic/scic abbreviation recognition.

TreeDist 2.1.0 2021-07-12

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.

TreeDist 2.0.3 2021-01-31

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

  • Explicitly import shiny/shinyjs functions.

TreeDist 2.0.0 2021-01-20

  • 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.

TreeDist 1.2.1 2020-09-17

  • Import RdMacros package ‘RdPack’.

TreeDist 1.2.0 2020-08-28

  • 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.

TreeDist 1.1.1 2020-07-10

  • Fix range errors when calculating tree distances.

TreeDist 1.1.0 Unreleased

TreeDist 1.0.0 2020-06-30

  • Initial release, building on some draft functions included in ‘TreeSearch’ 0.3.2.9005.