Files in treescape
Statistical Exploration of Landscapes of Phylogenetic Trees
inst
inst/shiny
inst/shiny/ui.R
inst/shiny/server.R
inst/shiny/www
inst/shiny/www/img
inst/shiny/www/img/logo.png
inst/shiny/www/img/line.png
inst/shiny/www/styles.css
inst/shiny/www/html
inst/shiny/www/html/help.html
inst/shiny/www/bootstrap.simplex.css
inst/doc
inst/doc/treescape.Rmd
inst/doc/DengueVignette.R
inst/doc/TransmissionTreesVignette.html
inst/doc/treescape.R
inst/doc/treescape.html
inst/doc/TransmissionTreesVignette.Rmd
inst/doc/TransmissionTreesVignette.R
inst/doc/DengueVignette.Rmd
inst/doc/DengueVignette.html
tests
tests/testthat.R
tests/testthat
tests/testthat/testbasics.R
src
src/RcppExports.cpp
src/CPP_update_combinations.cpp
NAMESPACE
data
data/DengueTrees.RData
data/fluTrees.RData
data/DengueBEASTMCC.RData
data/woodmiceTrees.RData
data/DengueSeqs.RData
R
R/findGroves.R
R/metrics.R
R/medTree.R
R/data.R
R/treescape.R
R/plotTreeDiff.R
R/transmissionTrees.R
R/RcppExports.R
R/servers.R
R/plotGroves.R
vignettes
vignettes/treescape.Rmd
vignettes/TransmissionTreesVignette.Rmd
vignettes/DengueVignette.Rmd
vignettes/figs
vignettes/figs/woodmice_plotTreeDiff-1.png
vignettes/figs/compare_BEAST_to_other_trees-2.png
vignettes/figs/woodmicePlots_readme-2.png
vignettes/figs/plotgroves_readme-1.png
vignettes/figs/plotgroves2_readme-2.png
vignettes/figs/distances-2.png
vignettes/figs/igraph_options-1.png
vignettes/figs/BEASTtree_diffs-1.png
vignettes/figs/plotgroves-1.png
vignettes/figs/woodmicePlots_readme-3.png
vignettes/figs/distances_readme-2.png
vignettes/figs/BEASTtree_diffs-2.png
vignettes/figs/see_ML_boots-1.png
vignettes/figs/construction.png
vignettes/figs/findgroves-with-emphasis_readme-1.png
vignettes/figs/compare_trees_NJ_v_ML-1.png
vignettes/figs/treescape3d.png
vignettes/figs/view_ML-1.png
vignettes/figs/plotgroves2_readme-3.png
vignettes/figs/compare_BEAST_to_other_trees-1.png
vignettes/figs/woodmiceMedian-1.png
vignettes/figs/plotgroves2_readme-1.png
vignettes/figs/wiw_MDS1000-1.png
vignettes/figs/distances-1.png
vignettes/figs/woodmiceCluster1_readme-1.png
vignettes/figs/woodmice-tip-emphasis_readme-1.png
vignettes/figs/woodmice_plotTreeDiff_readme-2.png
vignettes/figs/trees2_and_3-1.png
vignettes/figs/woodmiceMedian_readme-1.png
vignettes/figs/trees2_and_3-2.png
vignettes/figs/woodmice_plotTreeDiff_readme-1.png
vignettes/figs/woodmiceCluster1-1.png
vignettes/figs/treescapeTree.png
vignettes/figs/woodmice_plotTreeDiff-2.png
vignettes/figs/scree_plot-1.png
vignettes/figs/make_NJ-1.png
vignettes/figs/distances_readme-1.png
vignettes/figs/woodmicePlots_readme-1.png
vignettes/figs/see_NJ_boots-1.png
vignettes/figs/compare_BEAST_to_other_trees-3.png
vignettes/figs/treescapeDensiTree.png
vignettes/figs/wiwMedTreePlot-1.png
vignettes/figs/igraph_tree1-1.png
vignettes/DengueVignette.md
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/treescapeServer.Rd
man/plotGrovesD3.Rd
man/refTreeDist.Rd
man/plotTreeDiff.Rd
man/wiwTreeDist.Rd
man/treescape.Rd
man/multiDist.Rd
man/plotGroves.Rd
man/DengueSeqs.Rd
man/woodmiceTrees.Rd
man/medTree.Rd
man/findGroves.Rd
man/linearMrca.Rd
man/fluTrees.Rd
man/tipDiff.Rd
man/DengueBEASTMCC.Rd
man/treeVec.Rd
man/wiwMedTree.Rd
man/DengueTrees.Rd
man/findMRCIs.Rd
man/treeDist.Rd
