NEWS.md

In ms609/TreeDist: Calculate and Map Distances Between Phylogenetic Trees

TreeDist 2.7.0.9001 (development)

• Fix dead links in documentation

• Fix KCDiameter.multiPhylo() for multiple trees.

TreeDist 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).

TreeDist 2.6.3 (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)

• Support non-square matrices in LAPJV().

TreeDist 2.6.1 (2023-04-25)

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

• Use "PlotTools" package for spectrum legends.

• Minor documentation tweaks.

TreeDist 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.

TreeDist 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.

TreeDist 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++.

TreeDist 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.

TreeDist 2.3.0 (2022-01-04)

• 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)

• 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.

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.

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

• 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().

TreeDist 1.0.0 (2020-06-30)

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

ms609/TreeDist documentation built on April 5, 2024, 12:07 a.m.