Files in thibautjombart/treescape
Statistical Exploration of Landscapes of Phylogenetic Trees
.Rbuildignore
.Rhistory
.gitattributes
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
R/RcppExports.R
R/data.R
R/findGroves.R
R/medTree.R
R/metrics.R
R/plotGroves.R
R/plotTreeDiff.R
R/servers.R
R/transmissionTrees.R
R/treescape.R
README.Rmd
README.md
data/DengueBEASTMCC.RData
data/DengueSeqs.RData
data/DengueTrees.RData
data/fluTrees.RData
data/woodmiceTrees.RData
figures/figure1.png
figures/figureS1.png
figures/svg/baseimages/makeBaseImages.R
figures/svg/baseimages/mds.svg
figures/svg/baseimages/mdscolor.svg
figures/svg/baseimages/tree-1.svg
figures/svg/baseimages/tree-10.svg
figures/svg/baseimages/tree-2.svg
figures/svg/baseimages/tree-3.svg
figures/svg/baseimages/tree-4.svg
figures/svg/baseimages/tree-5.svg
figures/svg/baseimages/tree-6.svg
figures/svg/baseimages/tree-7.svg
figures/svg/baseimages/tree-8.svg
figures/svg/baseimages/tree-9.svg
figures/svg/figure1.svg
figures/svg/figureS1.svg
figures/svg/makeBaseImages.R
figures/svg/tablevalue.pdf
inst/doc/DengueVignette.html
inst/doc/TransmissionTreesVignette.html
inst/doc/treescape.html
inst/shiny/server.R
inst/shiny/ui.R
inst/shiny/www/bootstrap.simplex.css
inst/shiny/www/html/help.html
inst/shiny/www/img/line.png
inst/shiny/www/img/logo.png
inst/shiny/www/img/svg/main-images.svg
inst/shiny/www/img/svg/ygg.jpg
inst/shiny/www/styles.css
man/DengueBEASTMCC.Rd
man/DengueSeqs.Rd
man/DengueTrees.Rd
man/findGroves.Rd
man/findMRCIs.Rd
man/fluTrees.Rd
man/linearMrca.Rd
man/medTree.Rd
man/multiDist.Rd
man/plotGroves.Rd
man/plotGrovesD3.Rd
man/plotTreeDiff.Rd
man/refTreeDist.Rd
man/tipDiff.Rd
man/treeDist.Rd
man/treeVec.Rd
man/treescape.Rd
man/treescapeServer.Rd
man/wiwMedTree.Rd
man/wiwTreeDist.Rd
man/woodmiceTrees.Rd
src/.gitignore
src/CPP_update_combinations.cpp
src/RcppExports.cpp
tests/testthat.R
tests/testthat/testbasics.R
vignettes/DengueVignette.R
vignettes/DengueVignette.Rmd
vignettes/DengueVignette.html
vignettes/DengueVignette.md
vignettes/TransmissionTreesVignette.R
vignettes/TransmissionTreesVignette.Rmd
vignettes/TransmissionTreesVignette.html
vignettes/figs/BEASTtree_diffs-1.png
vignettes/figs/BEASTtree_diffs-2.png
vignettes/figs/compare_BEAST_to_other_trees-1.png
vignettes/figs/compare_BEAST_to_other_trees-2.png
vignettes/figs/compare_BEAST_to_other_trees-3.png
vignettes/figs/compare_trees_NJ_v_ML-1.png
vignettes/figs/construction.png
vignettes/figs/distances-1.png
vignettes/figs/distances-2.png
vignettes/figs/distances_readme-1.png
vignettes/figs/distances_readme-2.png
vignettes/figs/findgroves-with-emphasis_readme-1.png
vignettes/figs/igraph_options-1.png
vignettes/figs/igraph_tree1-1.png
vignettes/figs/make_NJ-1.png
vignettes/figs/plotgroves-1.png
vignettes/figs/plotgroves2_readme-1.png
vignettes/figs/plotgroves2_readme-2.png
vignettes/figs/plotgroves2_readme-3.png
vignettes/figs/plotgroves_readme-1.png
vignettes/figs/scree_plot-1.png
vignettes/figs/see_ML_boots-1.png
vignettes/figs/see_NJ_boots-1.png
vignettes/figs/trees2_and_3-1.png
vignettes/figs/trees2_and_3-2.png
vignettes/figs/treescape3d.png
vignettes/figs/treescapeDensiTree.png
vignettes/figs/treescapeTree.png
vignettes/figs/view_ML-1.png
vignettes/figs/wiwMedTreePlot-1.png
vignettes/figs/wiw_MDS1000-1.png
vignettes/figs/woodmice-tip-emphasis_readme-1.png
vignettes/figs/woodmiceCluster1-1.png
vignettes/figs/woodmiceCluster1_readme-1.png
vignettes/figs/woodmiceMedian-1.png
vignettes/figs/woodmiceMedian_readme-1.png
vignettes/figs/woodmicePlots_readme-1.png
vignettes/figs/woodmicePlots_readme-2.png
vignettes/figs/woodmicePlots_readme-3.png
vignettes/figs/woodmice_plotTreeDiff-1.png
vignettes/figs/woodmice_plotTreeDiff-2.png
vignettes/figs/woodmice_plotTreeDiff_readme-1.png
vignettes/figs/woodmice_plotTreeDiff_readme-2.png
vignettes/treescape.R
vignettes/treescape.Rmd
vignettes/treescape.html
