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[](https://ci.appveyor.com/project/thibautjombart/treespace/branch/master)
[](https://cran.r-project.org/package=treespace)
[](https://cran.r-project.org/package=treespace)
# *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*](https://cran.r-project.org/package=treespace/vignettes/introduction.html):
general introduction using a worked example.
- [*Dengue
example*](https://cran.r-project.org/package=treespace/vignettes/DengueVignette.html):
worked example using a Dengue dataset, used in the *treespace*
publication.
- [*transmission
trees*](https://cran.r-project.org/package=treespace/vignettes/TransmissionTreesVignette.html):
worked example using transmission trees.
- [*tip
categories*](https://cran.r-project.org/package=treespace/vignettes/tipCategories.html):
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](https://thibautjombart.github.io/treespace/CONDUCT.html). 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](https://github.com/thibautjombart/treespace/issues).
## Authors
Authors:
- [Thibaut Jombart](https://thibautjombart.netlify.app/)
- [Michelle Kendall](https://michellekendall.github.io/)
Contributors:
- [Jacob Almagro-Garcia](http://biotop.co/people/jacob-almagro/)
- [Caroline Colijn](https://www.sfu.ca/math/people/faculty/ccolijn/)
Maintainer of the CRAN version:
- [Michelle Kendall](https://michellekendall.github.io/)
See details of contributions on: <br>
<https://github.com/thibautjombart/treespace/graphs/contributors>
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