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.
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
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