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treebase (version 0.0-6)
An R package for discovery, access and manipulation of online phylogenies
Description
Interface to the API for TreeBASE
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Install
install.packages('treebase')
Monthly Downloads
407
Version
0.0-6
License
CC0
Issues
8
Pull Requests
0
Stars
10
Forks
4
Repository
http://www.github.com/ropensci/treebase
Maintainer
Carl Boettiger
Last Published
June 27th, 2012
Functions in treebase (0.0-6)
Search functions
metadata
metadata.rda
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.
oai_metadata
Search the OAI-PMH metadata by date, publisher, or identifier
treebase
treebase.rda
dryad_metadata
Search the dryad metadata archive
metadata_from_oai
Internal function for OAI-MPH interface to the Dryad database
drop_nontrees
drop errors from the search
clean_data
clean the fish.base data into pure ASCII
get_nex
imports phylogenetic trees from treebase. internal function
drop_nonascii
remove non-ASCII characters
have_branchlength
Simple function to identify which trees have branch lengths
get_study_id
return the study.id from the search results.
phylo_metadata
Search the PhyloWS metadata
cache_treebase
A function to cache the phylogenies in treebase locally
download_metadata
Download the metadata on treebase using the OAI-MPH interface
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