treescape: Statistical Exploration of Landscapes of Phylogenetic Trees

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

Author
Thibaut Jombart [aut], Michelle Kendall [aut, cre], Jacob Almagro-Garcia [aut], Caroline Colijn [aut]
Date of publication
2016-09-29 17:31:27
Maintainer
Michelle Kendall <m.kendall@imperial.ac.uk>
License
GPL (>= 2)
Version
1.10.17

View on CRAN

Man pages

DengueBEASTMCC
Dengue fever BEAST MCC tree
DengueSeqs
Dengue fever sequences
DengueTrees
BEAST analysis of Dengue fever
findGroves
Identify clusters of similar trees
findMRCIs
Find MRCIs
fluTrees
BEAST analysis of seasonal influenza (A/H3N2)
linearMrca
Linear MRCA function
medTree
Geometric median tree function
multiDist
Metric function for 'multiPhylo' input
plotGroves
Scatterplot of groups of trees
plotGrovesD3
Scatterplot of groups of trees using 'scatterD3'
plotTreeDiff
Plot tree differences
refTreeDist
Metric function for comparing a reference 'phylo' to...
tipDiff
Find tip position differences
treeDist
Metric function
treescape
Phylogenetic tree exploration
treescapeServer
Web-based tree explorer
treeVec
Tree vector function
wiwMedTree
Median transmission tree
wiwTreeDist
Transmission tree distance
woodmiceTrees
Bootstrap trees from woodmouse dataset

Files in this package

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/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