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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

## 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 ade4

Content overview

The main functions implemented in treespace are:

Other functions are central to the computations of distances between trees:

Distributed datasets include:

Documentation

treespace comes with the following vignettes:

Contributing / asking a question

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

Authors:

Contributors:

Maintainer of the CRAN version:

See details of contributions on:
https://github.com/thibautjombart/treespace/graphs/contributors