├── .Rbuildignore ├── .covrignore ├── .gitattributes ├── .github ├── copilot-instructions.md └── workflows │ ├── ASan.yml │ ├── R-CMD-check.yml │ ├── RcppDeepState.yml │ ├── benchmark.yml │ ├── codemeta.yml │ ├── copilot-setup-steps.yml │ ├── memcheck.yml │ ├── pkgdown.yml │ ├── revdepcheck.yml │ ├── rhub.yaml │ └── update-csl.yml ├── .gitignore ├── .lintr ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── DESCRIPTION ├── NAMESPACE ├── NEWS.md ├── R ├── HPart.R ├── Information.R ├── Islands.R ├── MSTSegments.R ├── Plot3.R ├── RcppExports.R ├── Reduce.R ├── TreeDist-package.R ├── VisualizeMatching.R ├── cluster_stats.R ├── hierarchical_mutual_information.R ├── kmeanspp.R ├── lap.R ├── median.R ├── parallel.R ├── plot.R ├── shiny.R ├── spectral_clustering.R ├── tree_distance.R ├── tree_distance_info.R ├── tree_distance_kendall-colijn.R ├── tree_distance_mast.R ├── tree_distance_msd.R ├── tree_distance_msi.R ├── tree_distance_nni.R ├── tree_distance_nye.R ├── tree_distance_path.R ├── tree_distance_rf.R ├── tree_distance_spr.R ├── tree_distance_utilities.R ├── tree_information.R ├── trustworthiness.R └── zzz.R ├── README.md ├── TreeDist.Rproj ├── benchmark ├── _compare_results.R ├── _init.R ├── _run_benchmarks.R ├── bench-LAPJV.R ├── bench-PathDist.R └── bench-tree-distances.R ├── codemeta.json ├── cran-comments.md ├── inst ├── CITATION ├── REFERENCES.bib ├── WORDLIST ├── _pkgdown.yml ├── apa-old-doi-prefix.csl ├── preamble.tex └── treespace │ ├── app.R │ └── www │ └── treespace.css ├── man-roxygen ├── MRS.R ├── distReturn.R ├── nTipParam.R ├── split12Params.R ├── splits12params.R ├── splitsParam.R ├── sprint.R ├── tree12ListParams.R └── tree12Params.R ├── man ├── AllSplitPairings.Rd ├── CalculateTreeDistance.Rd ├── CompareAll.Rd ├── Entropy.Rd ├── GeneralizedRF.Rd ├── HH.Rd ├── HPart.Rd ├── HierarchicalMutualInfo.Rd ├── HierarchicalMutualInformation.Rd ├── Islands.Rd ├── JaccardRobinsonFoulds.Rd ├── KMeansPP.Rd ├── KendallColijn.Rd ├── LAPJV.Rd ├── MASTSize.Rd ├── MSTSegments.Rd ├── MapTrees.Rd ├── MappingQuality.Rd ├── MatchingSplitDistance.Rd ├── MeilaVariationOfInformation.Rd ├── NNIDist.Rd ├── NormalizeInfo.Rd ├── NyeSimilarity.Rd ├── PathDist.Rd ├── Plot3.Rd ├── ReduceTrees.Rd ├── ReportMatching.Rd ├── Robinson-Foulds.Rd ├── SPRDist.Rd ├── SpectralEigens.Rd ├── SplitEntropy.Rd ├── SplitSharedInformation.Rd ├── SplitsCompatible.Rd ├── StartParallel.Rd ├── TreeDist-package.Rd ├── TreeDistPlot.Rd ├── TreeDistance.Rd ├── TreeInfo.Rd ├── VisualizeMatching.Rd ├── clone.Rd ├── cluster-statistics.Rd ├── dot-MASTSizeEdges.Rd ├── dot-PairMean.Rd ├── dot-TreeDistance.Rd ├── entropy_int.Rd ├── figures │ └── CID_talk.png └── median.multiPhylo.Rd ├── memcheck ├── all.R ├── examples.R ├── tests.R └── vignettes.R ├── src ├── RcppExports.cpp ├── day_1985.cpp ├── hmi.cpp ├── hpart.cpp ├── hpart.h ├── hpart_relabel.cpp ├── information.h ├── ints.h ├── lap.cpp ├── li_diameters.h ├── mast.cpp ├── nni_distance.cpp ├── path_vector.cpp ├── reduce_tree.cpp ├── reduce_tree.h ├── spr.cpp ├── tree_distance_functions.cpp ├── tree_distances.cpp └── tree_distances.h ├── tests ├── benchmark │ └── benchmark.R ├── figs │ └── plot-r │ │ ├── jrf-vm-matchzeros-false.svg │ │ ├── rf-collapse-a-node.svg │ │ ├── rf-collapse-and-change.svg │ │ ├── rf-vm-single-splits-plainedges.svg │ │ ├── test-lc-letters.svg │ │ ├── test-uc-letters.svg │ │ ├── test-vm.svg │ │ ├── test-vmr.svg │ │ ├── test-with-space.svg │ │ ├── test-without-space.svg │ │ └── visualize-mci-matching.svg ├── spelling.R ├── testthat.R └── testthat │ ├── _snaps │ ├── HPart │ │ └── plot-hpart.svg │ ├── MSTSegments │ │ └── mst-example-plot.svg │ ├── Plot3 │ │ ├── plotting-order.svg │ │ └── simple-plot.svg │ ├── VisualizeMatching │ │ ├── hidden-edge-labels.svg │ │ ├── jrf-vm-matchzeros-false.svg │ │ ├── rf-collapse-a-node.svg │ │ ├── rf-collapse-and-change.svg │ │ ├── rf-vm-single-splits-plainedges.svg │ │ ├── test-vm.svg │ │ ├── test-vmr.svg │ │ ├── visualize-mci-matching.svg │ │ ├── vm-one-rooted.svg │ │ └── vm-unrooted.svg │ └── plot │ │ ├── test-lc-letters.svg │ │ ├── test-uc-letters.svg │ │ ├── test-with-space.svg │ │ └── test-without-space.svg │ ├── test-64.R │ ├── test-HPart.R │ ├── test-Islands.R │ ├── test-MSTSegments.R │ ├── test-Plot3.R │ ├── test-Reduce.R │ ├── test-VisualizeMatching.R │ ├── test-cluster_stats.R │ ├── test-day_1985.cpp.r │ ├── test-different-tips.R │ ├── test-hierarchical_mutual_information.R │ ├── test-hmi.cpp.R │ ├── test-information.R │ ├── test-kmeanspp.R │ ├── test-lap.R │ ├── test-mast.R │ ├── test-median.R │ ├── test-parallel.R │ ├── test-plot.R │ ├── test-real-data.R │ ├── test-spectral_clustering.R │ ├── test-split_info.R │ ├── test-tree_distance.R │ ├── test-tree_distance_kc.R │ ├── test-tree_distance_nni.R │ ├── test-tree_distance_path.R │ ├── test-tree_distance_spr.R │ ├── test-tree_distance_utilities.R │ ├── test-tree_information.R │ ├── test-tree_shape.R │ └── test-trustworthiness.R └── vignettes ├── Batch1.svg ├── 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