Files in TreeDist

Calculate and Map Distances Between Phylogenetic Trees

MD5

NEWS.md

NAMESPACE

DESCRIPTION

R/RcppExports.R R/tree_distance.R R/kmeanspp.R R/Information.R R/shiny.R R/parallel.R R/tree_distance_msi.R R/tree_distance_nye.R R/tree_information.R R/tree_distance_rf.R R/tree_distance_utilities.R R/tree_distance_msd.R R/trustworthiness.R R/tree_distance_spr.R R/Plot3.R R/plot.R R/tree_distance_path.R R/tree_distance_nni.R R/MSTSegments.R R/tree_distance_kendall-colijn.R R/median.R R/tree_distance_info.R R/lap.R R/zzz.R R/spectral_clustering.R R/TreeDist-package.R R/tree_distance_mast.R R/cluster_stats.R R/VisualizeMatching.R

src/tree_distance_functions.cpp

src/RcppExports.cpp

src/tree_distances.h

src/day_1985.cpp

src/lap.cpp

src/nni_distance.cpp

src/ints.h

src/information.h

src/tree_distances.cpp

src/mast.cpp

inst/preamble.tex

inst/REFERENCES.bib

inst/CITATION

inst/WORDLIST

inst/apa-old-doi-prefix.csl

inst/doc/Generalized-RF.Rmd

inst/doc/Using-TreeDist.html

inst/doc/Generalized-RF.html

inst/doc/different-leaves.Rmd inst/doc/treespace.R inst/doc/information.Rmd

inst/doc/using-distances.html

inst/doc/landscapes.R inst/doc/using-distances.Rmd inst/doc/Using-TreeDist.Rmd inst/doc/Robinson-Foulds.R

inst/doc/landscapes.html

inst/doc/Robinson-Foulds.Rmd

inst/doc/Robinson-Foulds.html

inst/doc/using-distances.R inst/doc/Generalized-RF.R inst/doc/compare-treesets.R inst/doc/compare-treesets.Rmd

inst/doc/treespace.html

inst/doc/landscapes.Rmd

inst/doc/compare-treesets.html

inst/doc/treespace.Rmd

inst/doc/different-leaves.html

inst/doc/information.R inst/doc/different-leaves.R inst/doc/Using-TreeDist.R

inst/doc/information.html

inst/treespace/app.R

inst/treespace/www/treespace.css

build/vignette.rds

build/partial.rdb

tests/testthat.R tests/spelling.R tests/testthat/test-tree_distance.R tests/testthat/test-tree_distance_spr.R tests/testthat/test-plot.R tests/testthat/test-real-data.R tests/testthat/test-mast.R tests/testthat/test-cluster_stats.R tests/testthat/test-kmeanspp.R tests/testthat/test-tree_distance_utilities.R tests/testthat/test-64.R tests/testthat/test-tree_distance_path.R tests/testthat/test-median.R tests/testthat/test-MSTSegments.R tests/testthat/test-lap.R tests/testthat/test-trustworthiness.R tests/testthat/test-tree_distance_kc.R tests/testthat/test-VisualizeMatching.R tests/testthat/test-parallel.R tests/testthat/test-day_1985.cpp.r tests/testthat/test-tree_distance_nni.R tests/testthat/test-tree_shape.R tests/testthat/test-tree_information.R tests/testthat/test-information.R tests/testthat/test-Plot3.R tests/testthat/test-different-tips.R tests/testthat/test-split_info.R

tests/testthat/_snaps/Plot3/simple-plot.svg

tests/testthat/_snaps/Plot3/plotting-order.svg

tests/testthat/_snaps/MSTSegments/mst-example-plot.svg

tests/testthat/_snaps/VisualizeMatching/rf-vm-single-splits-plainedges.svg

tests/testthat/_snaps/VisualizeMatching/vm-one-rooted.svg

tests/testthat/_snaps/VisualizeMatching/visualize-mci-matching.svg

tests/testthat/_snaps/VisualizeMatching/test-vmr.svg

tests/testthat/_snaps/VisualizeMatching/rf-collapse-a-node.svg

tests/testthat/_snaps/VisualizeMatching/jrf-vm-matchzeros-false.svg

tests/testthat/_snaps/VisualizeMatching/test-vm.svg

tests/testthat/_snaps/VisualizeMatching/vm-unrooted.svg

tests/testthat/_snaps/VisualizeMatching/rf-collapse-and-change.svg

tests/testthat/_snaps/plot/test-with-space.svg

tests/testthat/_snaps/plot/test-uc-letters.svg

tests/testthat/_snaps/plot/test-without-space.svg

tests/testthat/_snaps/plot/test-lc-letters.svg

tests/benchmark/benchmark.R

tests/figs/plot-r/rf-vm-single-splits-plainedges.svg

tests/figs/plot-r/visualize-mci-matching.svg

tests/figs/plot-r/test-vmr.svg

tests/figs/plot-r/test-with-space.svg

tests/figs/plot-r/rf-collapse-a-node.svg

tests/figs/plot-r/jrf-vm-matchzeros-false.svg

tests/figs/plot-r/test-uc-letters.svg

tests/figs/plot-r/test-without-space.svg

tests/figs/plot-r/test-vm.svg

tests/figs/plot-r/rf-collapse-and-change.svg

tests/figs/plot-r/test-lc-letters.svg

vignettes/Generalized-RF.Rmd vignettes/different-leaves.Rmd vignettes/information.Rmd vignettes/using-distances.Rmd vignettes/Using-TreeDist.Rmd vignettes/Robinson-Foulds.Rmd

vignettes/CID_talk.png

vignettes/Batch2.svg

vignettes/compare-treesets.Rmd vignettes/landscapes.Rmd vignettes/treespace.Rmd

vignettes/Batch1.svg

man/TreeDist-package.Rd man/MatchingSplitDistance.Rd man/cluster-statistics.Rd man/NyeSimilarity.Rd man/Robinson-Foulds.Rd man/CalculateTreeDistance.Rd man/AllSplitPairings.Rd man/dot-PairMean.Rd man/SplitsCompatible.Rd man/KendallColijn.Rd man/NormalizeInfo.Rd man/KMeansPP.Rd man/TreeDistPlot.Rd man/GeneralizedRF.Rd man/MappingQuality.Rd man/PathDist.Rd man/dot-TreeDistance.Rd man/VisualizeMatching.Rd man/NNIDist.Rd man/MapTrees.Rd man/StartParallel.Rd man/CompareAll.Rd man/MeilaVariationOfInformation.Rd man/dot-MASTSizeEdges.Rd man/JaccardRobinsonFoulds.Rd man/SplitEntropy.Rd man/TreeInfo.Rd man/ReportMatching.Rd man/median.multiPhylo.Rd man/SPRDist.Rd man/SplitSharedInformation.Rd man/MASTSize.Rd man/MSTSegments.Rd man/Entropy.Rd man/LAPJV.Rd man/Plot3.Rd man/TreeDistance.Rd man/SpectralEigens.Rd

man/figures/CID_talk.png

TreeDist documentation built on Oct. 26, 2023, 1:07 a.m.