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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
## 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
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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