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treebase

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

  • [Publication in Methods in Ecology and Evolution doi:10.1111/j.2041-210X.2012.00247.x

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("ropensci/treebase")

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.

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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Install

install.packages('treebase')

Monthly Downloads

287

Version

0.1.5

License

CC0

Issues

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Maintainer

Last Published

February 16th, 2024

Functions in treebase (0.1.5)

cache_treebase

A function to cache the phylogenies in treebase locally
dryad_metadata

Search the dryad metadata archive
drop_nonascii

remove non-ASCII characters
drop_nontrees

drop errors from the search
download_metadata

Download the metadata on treebase using the OAI-MPH interface
have_branchlength

Simple function to identify which trees have branch lengths
get_study_id

return the study.id from the search results.
clean_data

clean the fish.base data into pure ASCII
phylo_metadata

Search the PhyloWS metadata
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.
show_metadata

Get the metadata associated with the study in which the phylogeny was published.
search_treebase

A function to pull in the phyologeny/phylogenies matching a search query
metadata

metadata.rda
get_nex

imports phylogenetic trees from treebase. internal function
treebase

treebase.rda
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