Interface to the API for TreeBASE
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("treebase", "ropensci")
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
cache_treebase: A function to cache the phylogenies in treebase locally
clean_data: clean the fish.base data into pure ASCII
drop_nonascii: remove non-ASCII characters
drop_nontrees: drop errors from the search
dryad_metadata: Search the dryad metadata archive
get_nex: imports phylogenetic trees from treebase. internal function
get_study: return the trees in treebase that correspond to the search results get_study is deprecated, and now can be performed more easily using phylo_metadata and oai_metadata search functions.
get_study_id: return the study.id from the search results.
have_branchlength: Simple function to identify which trees have branch lengths
metadata_from_oai: Internal function for OAI-MPH interface to the Dryad database
oai_metadata: Search the OAI-PMH metadata by date, publisher, or identifier
phylo_metadata: Search the PhyloWS metadata
search_metadata: Search the metadata on treebase using the OAI-MPH interface
search_treebase: A function to pull in the phyologeny/phylogenies matching a search query
show_metadata: Get the metadata associated with the study in which the phylogeny was published.