Skip to content

ropensci/treebase

master
Switch branches/tags

Name already in use

A tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. Are you sure you want to create this branch?
Code

Latest commit

 

Git stats

Files

Permalink
Failed to load latest commit information.
Type
Name
Latest commit message
Commit time
R
 
 
 
 
 
 
man
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

treebase

Build Status Build status

An R package for discovery, access and manipulation of online phylogenies

Installation

treebase is available from CRAN. You can install the latest version from the development website on github using the devtools package from within R. Make sure you have the latest version for the best experience.

library(devtools)
install_github("ropensci/treebase")

Getting Started

Use of the treebase package should be relatively straight forward:

library(treebase)
Phylogenies_from_Huelsenbeck <- search_treebase("Huelsenbeck", "author")

More interesting examples will take advantage of R to loop over large amounts of treebase data that would be to tiresome to search for, download and analyze by hand. Welcome to the era of big data phylogenetics.

  • Browse the examples in the documentation

  • We are preparing a short manuscript to introduce the motivation, functions, and use-cases for the treebase package. Meanwhile, a preprint is available as a dynamic document, where all of the examples shown are produced by the code shown using knitr. See source code.

  • treebase is part of the rOpenSci Project

References

  • Carl Boettiger, Duncan Temple Lang (2012). Treebase: An R package for discovery, access and manipulation of online phylogenies, Methods in Ecology and Evolution. doi:10.1111/j.2041-210X.2012.00247.x

About

An R interface to the treeBASE API (now on CRAN)

Topics

Resources

License

Code of conduct

Stars

Watchers

Forks

Packages

No packages published

Languages