Discovery, Access and Manipulation of 'TreeBASE' Phylogenies

Interface to the API for 'TreeBASE' < http://treebase.org> from 'R.' 'TreeBASE' is a repository of user-submitted phylogenetic trees (of species, population, or genes) and the data used to create them.


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

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")

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.
  • 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

News

Declare VignetteBuilder

2016-04-13

  • bugfix for performance issues on downloading trees
  • Make tests run on CRAN faster and more robust
  • update unit test structure for newer testthat version
  • switch to semantic version numbering
  • Rely on new Authors@R only
  • exclude unnecessary files
  • Improved error handling
  • Will allow multiple attempts if fails to access resource
  • Search now supports query by doi
  • updated caches
  • outdated demos removed

Reference manual

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install.packages("treebase")

0.1.4 by Carl Boettiger, 4 months ago


https://github.com/ropensci/treebase


Report a bug at http://www.github.com/ropensci/treebase/issues


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


Authors: Carl Boettiger [aut, cre], Duncan Temple Lang [aut]


Documentation:   PDF Manual  


Task views: Phylogenetics, Especially Comparative Methods


CC0 license


Imports XML, RCurl, methods, utils, httr

Depends on ape

Suggests testthat, knitr, rmarkdown


See at CRAN