treescape: Statistical Exploration of Landscapes of Phylogenetic Trees
Version 1.10.18

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

Browse man pages Browse package API and functions Browse package files

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("treescape")

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

Functions

DengueBEASTMCC Man page
DengueSeqs Man page
DengueTrees Man page
findGroves Man page Source code
findMRCIs Man page
fluTrees Man page
linearMrca Man page Source code
medTree Man page Source code
multiDist Man page Source code
plotGroves Man page Source code
plotGrovesD3 Man page Source code
plotTreeDiff Man page Source code
refTreeDist Man page Source code
render.server.info Source code
tipDiff Man page Source code
treeDist Man page Source code
treeVec Man page Source code
treescape Man page Source code
treescapeServer Man page Source code
updateDistancesWithCombinations Source code
wiwMedTree Man page
wiwTreeDist Man page
woodmiceTrees Man page

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
treescape documentation built on May 19, 2017, 3:32 p.m.