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()'.

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

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

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