Tools for the exploration of distributions of phylogenetic trees.
This package includes a 'shiny' interface which can be started from R using
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:
The stable version can be installed from CRAN using:
Then, to load the package, use:
## 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
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
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
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
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.
Maintainer of the CRAN version:
See details of contributions on: