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

treebase

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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("treebase", "ropensci")

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
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