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 treespaceServer().


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treespace: exploration of landscapes of phylogenetic trees

treespace implements new methods for the exploration and analysis of distributions of phylogenetic trees for a given set of taxa.

Installing treespace

To install the development version from github:

library(devtools)
install_github("thibautjombart/treespace")

The stable version can be installed from CRAN using:

install.packages("treespace")

Then, to load the package, use:

library("treespace")
## Loading required package: ade4
## Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'

Content overview

The main functions implemented in treespace are:

  • treespace: explore landscapes of phylogenetic trees

  • treespaceServer: open up an application in a web browser for an interactive exploration of the diversity in a set of trees

  • findGroves: identify clusters of similar trees

  • plotGroves: scatterplot of groups of trees, and plotGrovesD3 which enables interactive plotting based on d3.js

  • medTree: find geometric median tree(s) to summarise a group of trees

  • wiwTreeDist: find the distance between transmission trees by comparing their MRCI depth matrices

  • wiwMedTree: find the median of a list of transmission scenarios

  • relatedTreeDist: calculate the distances between trees whose tips belong to the same categories but are not necessarily identically labelled

  • treeConcordance: calculate the concordance between a category tree and an individuals tree

Other functions are central to the computations of distances between trees:

  • treeVec: characterise a tree by a vector

  • treeDist: find the distance between two tree vectors

  • multiDist: find the pairwise distances of a list of trees

  • refTreeDist: find the distances of a list of trees from a reference tree

  • tipDiff: for a pair of trees, list the tips with differing ancestry

  • plotTreeDiff: plot a pair of trees, highlighting the tips with differing ancestry

  • findMRCIs: find the most recent common infector (MRCI) matrix from "who infected whom" information

  • tipsMRCAdepths: similar to treeVec but the output is a matrix where columns 1 and 2 correspond to tip labels and column 3 gives the depth of the MRCA of that pair of tips

Distributed datasets include:

  • woodmiceTrees: illustrative set of 201 trees built using the neighbour-joining and bootstrapping example from the woodmice dataset in the ape documentation.

  • DengueTrees: 500 trees sampled from a BEAST posterior set of trees from (Drummond and Rambaut, 2007)

  • DengueSeqs: 17 dengue virus serotype 4 sequences from (Lanciotti et al., 1997), from which the DengueTrees were inferred.

  • DengueBEASTMCC: the maximum clade credibility (MCC) tree from the DengueTrees.


Documentation

treespace is fully documented on a dedicated website.

It also comes with the following vignettes:

  • introduction: general introduction using a worked example.

  • Dengue example: worked example using a Dengue dataset, used in the treespace publication.

  • transmission trees: worked example using transmission trees.

  • tip categories: introduction to the measures for comparing trees with shared tip label "categories"

Contributing / asking a question

Contributions are welcome via pull requests.

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

Questions, feature requests and bugs can be reported using the package's issue system.

Authors

Authors:

Contributors:

Maintainer of the CRAN version:

See details of contributions on:
https://github.com/thibautjombart/treespace/graphs/contributors

News

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("treespace")

1.1.1 by Michelle Kendall, a month ago


Browse source code at https://github.com/cran/treespace


Authors: Thibaut Jombart [aut], Michelle Kendall [aut, cre], Jacob Almagro-Garcia [aut], Caroline Colijn [aut]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports adegenet, adegraphics, adephylo, combinat, compiler, distory, fields, htmlwidgets, MASS, parallel, phangorn, phytools, Rcpp, RLumShiny, scatterD3, shiny, shinyBS, utils

Depends on ape, ade4

Suggests ggplot2, igraph, knitr, pander, RColorBrewer, reshape2, rgl, rmarkdown, testthat

Linking to Rcpp


See at CRAN