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: ape
## Loading required package: ade4
## Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
## Registered S3 method overwritten by 'spdep':
## method from
## plot.mst ape
## 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 ade4The 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 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