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treebase (version 0.1.1)

Discovery, Access and Manipulation of 'TreeBASE' Phylogenies

Description

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.

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Install

install.packages('treebase')

Monthly Downloads

217

Version

0.1.1

License

CC0

Issues

7

Pull Requests

0

Stars

10

Forks

4

Maintainer

Carl Boettiger

Last Published

June 16th, 2015

Functions in treebase (0.1.1)

metadata

metadata.rda
search_treebase

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

treebase.rda
oai_metadata

Search the OAI-PMH metadata by date, publisher, or identifier
show_metadata

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

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

Simple function to identify which trees have branch lengths
cache_treebase

A function to cache the phylogenies in treebase locally
dryad_metadata

Search the dryad metadata archive
phylo_metadata

Search the PhyloWS metadata
drop_nontrees

drop errors from the search
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.
metadata_from_oai

Internal function for OAI-MPH interface to the Dryad database
clean_data

clean the fish.base data into pure ASCII
drop_nonascii

remove non-ASCII characters
get_study_id

return the study.id from the search results.