Files in ms609/TreeDist
Calculate and Map Distances Between Phylogenetic Trees
.Rbuildignore
.covrignore
.gitattributes
.github/workflows/R-CMD-check.yml
.github/workflows/RcppDeepState.yml
.github/workflows/codemeta.yml
.github/workflows/memcheck.yml
.github/workflows/pkgdown.yml
.github/workflows/revdepcheck.yml
.github/workflows/rhub.yaml
.gitignore
CODE_OF_CONDUCT.md
CONTRIBUTING.md
DESCRIPTION
NAMESPACE
NEWS.md
R/Information.R
R/MSTSegments.R
R/Plot3.R
R/RcppExports.R
R/TreeDist-package.R
R/VisualizeMatching.R
R/cluster_stats.R
R/kmeanspp.R
R/lap.R
R/median.R
R/parallel.R
R/plot.R
R/shiny.R
R/spectral_clustering.R
R/tree_distance.R
R/tree_distance_info.R
R/tree_distance_kendall-colijn.R
R/tree_distance_mast.R
R/tree_distance_msd.R
R/tree_distance_msi.R
R/tree_distance_nni.R
R/tree_distance_nye.R
R/tree_distance_path.R
R/tree_distance_rf.R
R/tree_distance_spr.R
R/tree_distance_utilities.R
R/tree_information.R
R/trustworthiness.R
R/zzz.R
README.md
TreeDist.Rproj
codemeta.json
cran-comments.md
inst/CITATION
inst/REFERENCES.bib
inst/WORDLIST
inst/_pkgdown.yml
inst/apa-old-doi-prefix.csl
inst/preamble.tex
inst/treespace/app.R
inst/treespace/www/treespace.css
man-roxygen/MRS.R
man-roxygen/distReturn.R
man-roxygen/nTipParam.R
man-roxygen/split12Params.R
man-roxygen/splits12params.R
man-roxygen/splitsParam.R
man-roxygen/tree12ListParams.R
man-roxygen/tree12Params.R
man/AllSplitPairings.Rd
man/CalculateTreeDistance.Rd
man/CompareAll.Rd
man/Entropy.Rd
man/GeneralizedRF.Rd
man/JaccardRobinsonFoulds.Rd
man/KendallColijn.Rd
man/LAPJV.Rd
man/MASTSize.Rd
man/MSTSegments.Rd
man/MapTrees.Rd
man/MappingQuality.Rd
man/MatchingSplitDistance.Rd
man/MeilaVariationOfInformation.Rd
man/NNIDist.Rd
man/NormalizeInfo.Rd
man/NyeSimilarity.Rd
man/PathDist.Rd
man/Plot3.Rd
man/ReportMatching.Rd
man/Robinson-Foulds.Rd
man/SPRDist.Rd
man/SpectralEigens.Rd
man/SplitEntropy.Rd
man/SplitSharedInformation.Rd
man/SplitsCompatible.Rd
man/StartParallel.Rd
man/TreeDist-package.Rd
man/TreeDistPlot.Rd
man/TreeDistance.Rd
man/TreeInfo.Rd
man/VisualizeMatching.Rd
man/cluster-statistics.Rd
man/dot-MASTSizeEdges.Rd
man/dot-PairMean.Rd
man/dot-TreeDistance.Rd
man/figures/CID_talk.png
man/kmeanspp.Rd
man/median.multiPhylo.Rd
memcheck/all.R
memcheck/examples.R
memcheck/tests.R
memcheck/vignettes.R
src/RcppExports.cpp
src/day_1985.cpp
src/information.h
src/ints.h
src/lap.cpp
src/mast.cpp
src/nni_distance.cpp
src/tree_distance_functions.cpp
src/tree_distances.cpp
src/tree_distances.h
tests/benchmark/benchmark.R
tests/figs/plot-r/jrf-vm-matchzeros-false.svg
tests/figs/plot-r/rf-collapse-a-node.svg
tests/figs/plot-r/rf-collapse-and-change.svg
tests/figs/plot-r/rf-vm-single-splits-plainedges.svg
tests/figs/plot-r/test-lc-letters.svg
tests/figs/plot-r/test-uc-letters.svg
tests/figs/plot-r/test-vm.svg
tests/figs/plot-r/test-vmr.svg
tests/figs/plot-r/test-with-space.svg
tests/figs/plot-r/test-without-space.svg
tests/figs/plot-r/visualize-mci-matching.svg
tests/spelling.R
tests/testthat.R
tests/testthat/_snaps/MSTSegments/mst-example-plot.svg
tests/testthat/_snaps/Plot3/plotting-order.svg
tests/testthat/_snaps/Plot3/simple-plot.svg
tests/testthat/_snaps/VisualizeMatching/jrf-vm-matchzeros-false.svg
tests/testthat/_snaps/VisualizeMatching/rf-collapse-a-node.svg
tests/testthat/_snaps/VisualizeMatching/rf-collapse-and-change.svg
tests/testthat/_snaps/VisualizeMatching/rf-vm-single-splits-plainedges.svg
tests/testthat/_snaps/VisualizeMatching/test-vm.svg
tests/testthat/_snaps/VisualizeMatching/test-vmr.svg
tests/testthat/_snaps/VisualizeMatching/visualize-mci-matching.svg
tests/testthat/_snaps/VisualizeMatching/vm-one-rooted.svg
tests/testthat/_snaps/VisualizeMatching/vm-unrooted.svg
tests/testthat/_snaps/plot/test-lc-letters.svg
tests/testthat/_snaps/plot/test-uc-letters.svg
tests/testthat/_snaps/plot/test-with-space.svg
tests/testthat/_snaps/plot/test-without-space.svg
tests/testthat/test-64.R
tests/testthat/test-MSTSegments.R
tests/testthat/test-Plot3.R
tests/testthat/test-VisualizeMatching.R
tests/testthat/test-cluster_stats.R
tests/testthat/test-day_1985.cpp.r
tests/testthat/test-different-tips.R
tests/testthat/test-information.R
tests/testthat/test-kmeanspp.R
tests/testthat/test-lap.R
tests/testthat/test-mast.R
tests/testthat/test-median.R
tests/testthat/test-parallel.R
tests/testthat/test-plot.R
tests/testthat/test-real-data.R
tests/testthat/test-split_info.R
tests/testthat/test-tree_distance.R
tests/testthat/test-tree_distance_kc.R
tests/testthat/test-tree_distance_nni.R
tests/testthat/test-tree_distance_path.R
tests/testthat/test-tree_distance_spr.R
tests/testthat/test-tree_distance_utilities.R
tests/testthat/test-tree_information.R
tests/testthat/test-tree_shape.R
tests/testthat/test-trustworthiness.R
vignettes/Batch1.svg
vignettes/Batch2.svg
vignettes/CID_talk.png
vignettes/Generalized-RF.Rmd
vignettes/Robinson-Foulds.Rmd
vignettes/Using-TreeDist.Rmd
vignettes/compare-treesets.Rmd
vignettes/different-leaves.Rmd
vignettes/information.Rmd
vignettes/landscapes.Rmd
vignettes/treespace.Rmd
vignettes/using-distances.Rmd
