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.
treebase is part of the rOpenSci Project