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: ape

## Loading required package: ade4

## Registered S3 methods overwritten by 'adegraphics':
##   method         from
##   biplot.dudi    ade4
##   kplot.foucart  ade4
##   kplot.mcoa     ade4
##   kplot.mfa      ade4
##   kplot.pta      ade4
##   kplot.sepan    ade4
##   kplot.statis   ade4
##   scatter.coa    ade4
##   scatter.dudi   ade4
##   scatter.nipals ade4
##   scatter.pco    ade4
##   score.acm      ade4
##   score.mix      ade4
##   score.pca      ade4
##   screeplot.dudi ade4

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 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:

• Thibaut Jombart

• Michelle Kendall

Contributors:

• Jacob Almagro-Garcia

• Caroline Colijn

Maintainer of the CRAN version:

• Michelle Kendall

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