The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.

treebase

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

• [Publication in Methods in Ecology and Evolution doi:10.1111/j.2041-210X.2012.00247.x

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.

• 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

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.