Changes in version 2.14.0.9001                     

  - Fixed PhylogeneticInformationDistance() miscalculating score for
    identical 4-leaf trees.

  - Improve KMeansPP() performance: O(k²×n) → O(k×n).

  - Tinkering to get web app working

                 Changes in version 2.14.0 (2026-05-09)                 

New features

  - TransferConsensus() constructs a consensus tree that minimizes the
    sum of transfer distances to a set of input trees, using a greedy
    add-and-prune heuristic. Unlike majority-rule consensus, which can
    be highly unresolved when phylogenetic signal is diffuse, the
    transfer consensus uses the finer-grained transfer distance to
    produce more resolved trees.

  - TransferDist() computes the transfer dissimilarity between
    phylogenetic trees, with scaled and unscaled variants. Supports
    all-pairs, cross-pairs, and single-pair computations.

  - LAP (Jonker–Volgenant linear assignment) and MCI (Mutual Clustering
    Information) C++ implementations are now exposed via
    inst/include/TreeDist/ headers, allowing downstream packages to use
    LinkingTo: TreeDist.

Internals

  - Large-tree support (requires TreeTools ≥ 2.3.0): all distance
    functions now accept trees with up to 32 767 tips (previously
    limited to SL_MAX_TIPS, 2048 with TreeTools ≤ 2.2.0).

  - Stack-allocated split buffers replaced with dynamically-sized
    vectors, removing a hard dependency on the compile-time
    SL_MAX_SPLITS constant. TreeDist now supports trees of any size
    permitted by TreeTools.

Performance

  - RobinsonFoulds() now uses a fast C++ batch path for cross-distance
    computations (tree list vs tree list), matching the existing
    all-pairs batch performance and providing a ~21× speedup on typical
    inputs.

                       Changes in version 2.13.0                        

New features

  - MCITree() selects the tree from a posterior sample with the highest
    total split information content — a Maximum Clade Information
    analogue of the Maximum Clade Credibility tree.

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

  - ClusteringInfoDistance(), DifferentPhylogeneticInfo(),
    MatchingSplitInfoDistance(), and InfoRobinsonFoulds() now avoid
    duplicate as.Splits() conversions and use C++ batch functions for
    per-tree entropy/information computation. This reduces R-level
    overhead by ~8–17% for typical analyses.

  - Cross-pairs computations (tree1 vs tree2 where both are lists) now
    use the same optimized batch path as all-pairs computations.

Kendall & Colijn 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()).

                 Changes in version 2.12.0 (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.

                 Changes in version 2.11.1 (2025-10-13)                 

  - Improve robustness of SpectralEigens() tests.

                 Changes in version 2.11.0 (2025-09-28)                 

  - HierarchicalMutualInformation() calculates the information shared
    between pairs of hierarchical partition structures
    \doi{10.1103/PhysRevE.92.062825}.

  - 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.

                 Changes in version 2.10.1 (2025-08-25)                 

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

                 Changes in version 2.10.0 (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.

                 Changes in version 2.9.2 (2025-01-11)                  

  - Fix crash when calculating NNI distance for large trees.

                 Changes in version 2.9.1 (2024-09-07)                  

  - Avoid false positive in MKL testing environment.

                 Changes in version 2.9.0 (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.

                 Changes in version 2.8.0 (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()

                        Changes in version 2.7.1                        

  - Documentation improvements.

  - Fix KCDiameter.multiPhylo() for multiple trees.

                 Changes in version 2.7.0 (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).

                 Changes in version 2.6.3 (2023-08-25)                  

  - Fix bug when comparing a "multiPhylo" object containing a single
    tree.

  - Documentation clarification: finding non-matching leaves.

                 Changes in version 2.6.2 (2023-06-29)                  

  - Support non-square matrices in LAPJV().

                 Changes in version 2.6.1 (2023-05-01)                  

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

  - Use "PlotTools" package for spectrum legends.

  - Minor documentation tweaks.

                 Changes in version 2.6.0 (2023-02-20)                  

  - Support comparison of trees with different tips.

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

  - Update tests for compatibility with ape 5.7.

                 Changes in version 2.5.0 (2022-10-07)                  

  - 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.

                 Changes in version 2.4.1 (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++.

                 Changes in version 2.4.0 (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.

                 Changes in version 2.3.0 (2022-01-03)                  

  - Support ConsensusInfo(p > 0.5).

  - Address hypervolume comparison in vignettes.

  - Support uniform manifold approximation and projection in app.

                 Changes in version 2.2.0 (2021-09-13)                  

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

  - Support for parallel computation via StartParallel().

  - Progress bars.

                 Changes in version 2.1.1 (2021-07-13)                  

  - Solaris compatibility.

  - Modest vignette improvements.

  - spic/scic abbreviation recognition.

                 Changes in version 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.

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.

                 Changes in version 2.0.3 (2021-01-31)                  

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

  - Explicitly import shiny/shinyjs functions.

                 Changes in version 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.

                 Changes in version 1.2.1 (2020-09-17)                  

  - Import RdMacros package 'RdPack'.

                 Changes in version 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.

                 Changes in version 1.1.1 (2020-07-10)                  

  - Fix range errors when calculating tree distances.

                        Changes in version 1.1.0                        

  - Improvements to NNIDist() in light of Fack et al. (2002).

  - Add NNIDiameter(): approximate diameter of NNI distance.

  - Remove vignette 'Interpreting tree distances': duplicates
    https://ms609.github.io/TreeDistData/articles/09-expected-similarity.html.

  - Remove redundant data object oneOverlap.

  - Fix an issue when installing on R 3.x (require C++11 to ensure
    declaration of UINT_FAST16_MAX).

  - Fix memory-handling bug in lapjv().

                 Changes in version 1.0.0 (2020-06-30)                  

  - Initial release, building on some draft functions included in
    'TreeSearch' 0.3.2.9005.