treebase compendium: publication, R package, version history
treebase
========
_An R package for discovery, access and manipulation of online phylogenies_
- [Publication in Methods in Ecology and Evolution](http://dx.doi.org/10.1111/j.2041-210X.2012.00247.x)
- [Development version source code on github](https://github.com/ropensci/treeBASE)
- [HTML package documentation](http://ropensci.github.com/treeBASE/)
- [Report issues, bugs or feature requests](https://github.com/ropensci/treebase/issues)
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.
'''r
library(devtools)
install_github("treebase", "ropensci")
'''
Getting Started
---------------
Use of the 'treebase' package should be relatively straight forward:
'''r
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](http://ropensci.github.com/treeBASE/)
- We are preparing a short manuscript to introduce the motivation, functions, and use-cases for the 'treebase' package. Meanwhile, a [preprint is available](https://github.com/ropensci/treeBASE/blob/master/inst/doc/treebase/treebase_github.md) as a dynamic document, where all of the examples shown are produced by the code shown using 'knitr'. [See source code](https://github.com/ropensci/treeBASE/blob/master/inst/doc/treebase/treebase.Rmd).
- treebase is part of the [rOpenSci Project](http://ropensci.github.com)
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
