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Changelog

Source: NEWS.md

TreeDist 2.13.0 (2026-03-17)

Performance

Pairwise distance computation has been substantially optimized. Typical speedups over v2.12.0 for tree sets where most splits are shared (MCMC posteriors, bootstrap replicates):

Metric 100 × 50 tips 40 × 200 tips
ClusteringInfoDistance ~5× ~12×
MatchingSplitDistance ~7× ~11×
InfoRobinsonFoulds ~4× ~5×
DifferentPhylogeneticInfo ~1.3× ~1.1×
MatchingSplitInfoDistance ~1.4× ~1×

OpenMP parallelism

  • All pairwise distance functions now use an OpenMP multi-threaded batch path when the package is compiled with OpenMP support, for both all-pairs and cross-pairs (tree1 vs tree2) computations.

  • The number of OpenMP threads is controlled by options(mc.cores = N); the default is 1 (single-threaded). Set mc.cores to parallel::detectCores() or a fixed integer to enable multi-threading. StartParallel() / StopParallel() are no longer needed when OpenMP is available.

Algorithmic improvements

  • Exact split matches between trees are now detected via an O(n log n) sort-and-merge pre-scan, reducing the linear assignment problem to only the unmatched splits. For tree sets with high split overlap, this yields the largest portion of the speedups above.

  • Internal lookup table for log₂ values shrunk from 32 MB to 16 KB, improving L1 cache locality for information-based distance metrics.

  • Information content accumulation in MutualClusteringInfo() rewritten as a branchless expression, reducing per-split-pair table lookups from 16 to 4 and eliminating 8 branches.

  • spi_overlap() (used by SharedPhylogeneticInfo(), MatchingSplitInfoDistance(), and JaccardRobinsonFoulds()) rewritten to use a single-pass hardware POPCNT approach, replacing the previous four-pass boolean scan.

  • Hardware POPCNT instruction now used on x86-64 via inline assembly (requires TreeTools ≥ 2.2).

  • Internal cost-matrix storage is now pooled across tree pairs within each thread, eliminating per-pair heap allocation overhead.

R-level fast paths

KendallColijn distance

  • KCVector() reimplemented in C++, giving ~220× speedup per tree.

  • All-pairs and cross-pairs KendallColijn() Euclidean distances now computed in C++ (pair_diff_euclidean(), vec_diff_euclidean()).

TreeDist 2.12.0 (2026-02-12)

CRAN release: 2026-02-13

  • Support larger trees in some functions by updating some functions to use 32-bit integers, per TreeTools v2.1.0.

  • AHMI() now returns negative values (previously zeroed in error).

  • Experimental support for a new method of SPR distance calculation: subject to change or removal.

TreeDist 2.11.1 (2025-10-13)

CRAN release: 2025-10-13

TreeDist 2.11.0 (2025-09-26)

CRAN release: 2025-09-28

  • HierarchicalMutualInformation() calculates the information shared between pairs of hierarchical partition structures .

  • Fix bug in calculation of MutualClusteringInfo(): the matching chosen was not always the global optimum, causing distances to be overestimated in some circumstances (#163).

  • Fix crash in robinson_foulds_all_pairs() and RobinsonFoulds(list).

  • Support larger trees in NNI distance calculations.

TreeDist 2.10.1 (2025-08-24)

CRAN release: 2025-08-25

  • Compiler-safe vector initialization, resolving M1-SAN warnings.

TreeDist 2.10.0 (2025-08-22)

CRAN release: 2025-08-22

Note - this release introduced a bug in the computation of the mutual clustering information / clustering information distance. The globally optimal matching between splits was not always found. This was fixed in v2.11.0.

  • Ntropy() computes entropy from integer counts.

  • C++ optimizations and reformatting:

    • Faster tree distance calculation.
    • 2x speed-up of LAPJV for large matrices.

  • Require R4.0; discontinue tests against R4.0.

TreeDist 2.9.2 (2025-01-11)

CRAN release: 2025-01-11

  • Fix crash when calculating NNI distance for large trees.

TreeDist 2.9.1 (2024-09-05)

CRAN release: 2024-09-07

  • Avoid false positive in MKL testing environment.

TreeDist 2.9.0 (2024-09-03)

CRAN release: 2024-09-03

  • VisualizeMatching() allows more control over output format, and returns the matching (#124).

  • DistanceFromMedian(Average = median) allows calculation of MAD.

  • SpectralEigens() returns correct eigenvalues (smallest was overlooked).

  • SpectralEigens() handles values of nEig larger than the input.

  • Anticipate new behaviour of unlist(use.names = TRUE) in R 4.5.

TreeDist 2.8.0 (2024-07-25)

CRAN release: 2024-07-26

  • Islands() allows the identification of islands of trees.

  • Internal implementation of path and SPR distances, removing dependency on phangorn (and thus R 4.4).

  • Add progress bar within .MaxValue()

TreeDist 2.7.1 (2024-06-13)

  • Documentation improvements.

  • Fix KCDiameter.multiPhylo() for multiple trees.

TreeDist 2.7.0 (2023-10-25)

CRAN release: 2023-10-25

  • Fix calculation error in StrainCol().

  • App: Display strain in 3D tree space viewer.

  • Support for distances between larger trees.

  • Support unrooted trees in VisualizeMatching() (#103).

TreeDist 2.6.3 (2023-08-25)

CRAN release: 2023-08-25

  • Fix bug when comparing a “multiPhylo” object containing a single tree.

  • Documentation clarification: finding non-matching leaves.

TreeDist 2.6.2 (2023-06-28)

CRAN release: 2023-06-29

  • Support non-square matrices in LAPJV().

TreeDist 2.6.1 (2023-04-25)

CRAN release: 2023-05-01

  • StopParallel() gains quietly argument to suppress unnecessary messages.

  • Use “PlotTools” package for spectrum legends.

  • Minor documentation tweaks.

TreeDist 2.6.0 (2023-02-20)

CRAN release: 2023-02-20

  • Support comparison of trees with different tips.

  • Fix caching errors in MapDist() (#98).

  • Update tests for compatibility with ape 5.7.

TreeDist 2.5.0 (2022-10-07)

CRAN release: 2022-10-07

TreeDist 2.4.1 (2022-07-20)

CRAN release: 2022-07-20

  • 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++.

TreeDist 2.4.0 (2022-03-23)

CRAN release: 2022-03-23

  • 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.

TreeDist 2.3.0 (2022-01-04)

CRAN release: 2022-01-03

  • Support ConsensusInfo(p > 0.5).

  • Address hypervolume comparison in vignettes.

  • Support uniform manifold approximation and projection in app.

TreeDist 2.2.0 (2021-09-13)

CRAN release: 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)

CRAN release: 2021-07-13

  • Solaris compatibility.

  • Modest vignette improvements.

  • spic/scic abbreviation recognition.

TreeDist 2.1.0 (2021-07-12)

CRAN release: 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.

Renamed functions

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)

CRAN release: 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)

CRAN release: 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)

CRAN release: 2020-09-17

  • Import RdMacros package ‘RdPack’.

TreeDist 1.2.0 (2020-08-28)

CRAN release: 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)

CRAN release: 2020-07-10

  • Fix range errors when calculating tree distances.

TreeDist 1.1.0

TreeDist 1.0.0 (2020-06-30)

CRAN release: 2020-06-30

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