treescape: Statistical Exploration of Landscapes of Phylogenetic Trees

Tools for the exploration of distributions of phylogenetic trees. This package includes a shiny interface which can be started from R using 'treescapeServer()'.

Install the latest version of this package by entering the following in R:
install.packages("treescape")
AuthorThibaut Jombart [aut], Michelle Kendall [aut, cre], Jacob Almagro-Garcia [aut], Caroline Colijn [aut]
Date of publication2016-12-08 15:30:03
MaintainerMichelle Kendall <m.kendall@imperial.ac.uk>
LicenseGPL (>= 2)
Version1.10.18

View on CRAN

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.