Tools for the exploration of distributions of phylogenetic trees.
This package includes a 'shiny' interface which can be started from R using
treespaceServer().
For further details see Jombart et al. (2017)
treespace implements new methods for the exploration and analysis of distributions of phylogenetic trees for a given set of taxa.
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'
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
.
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"
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:
Contributors:
Maintainer of the CRAN version:
See details of contributions on:
https://github.com/thibautjombart/treespace/graphs/contributors