Phylogenetic Tree Manipulation Class and Methods

S4 class and methods for intuitive and efficient phylogenetic tree manipulation.


Build StatusCoverage StatusCRAN downloadsRdoc

The treeman R package provides a list based class for encoding phylogenetic trees in R, making manipulating phylogenetic trees easier to code and more efficient to run. treeman is aimed to be fast, simple and intuitive.

Installation

With CRAN:

install.packages('treeman')

Installing the development copy via GitHub

library(devtools)
install_github('dombennett/treeman')

Quick guide

# working with the TreeMan class
library(treeman)
?TreeMan  # check the documentation
tree <- randTree(10)  # generate a random tree of 10 tips
summary(tree)  # check key stats
tree["tips"]  # extract key stats

For more details check out the wiki.

Licence

GPL-2

Status

Version 1.1 released.

Reference

Bennett, D.J., Sutton, M.D. & Turvey, S.T., 2017. treeman: an R package for efficient and intuitive manipulation of phylogenetic trees. BMC Research Notes, 10(1), p.30. Available online

Author

D.J. Bennett (but I welcome pull requests!)

News

Reference manual

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install.packages("treeman")

1.1.3 by D.J. Bennett, 5 months ago


Browse source code at https://github.com/cran/treeman


Authors: D.J. Bennett


Documentation:   PDF Manual  


GPL-2 license


Imports plyr, ape, RJSONIO, stringr, bigmemory

Depends on methods

Suggests testthat


Imported by phylotaR.


See at CRAN