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NEWS

• Avoid crashing when calculating NNI distance for large trees.

• Avoid false positive in MKL testing environment.

• 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.

• 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()

• Documentation improvements.

• Fix KCDiameter.multiPhylo() for multiple trees.

• 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).

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

• Documentation clarification: finding non-matching leaves.

• Support non-square matrices in LAPJV().

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

• Use “PlotTools” package for spectrum legends.

• Minor documentation tweaks.

• Support comparison of trees with different tips.

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

• Update tests for compatibility with ape 5.7.

• 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.

• 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++.

• 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.

• 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.

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

• SpectralClustering() re-named to SpectralEigens().

• 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.

• 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().

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

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