treebase 0.0-6

Interface to the API for TreeBASE

treebase

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

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("treebase", "ropensci")

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.

  • Browse the examples in the documentation
  • 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

Help topics

  • 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: metadata.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
  • 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.
  • treebase: treebase.rda

Vignettes

Demos

Dependencies

  • Depends: ape
  • Imports: XML, RCurl, methods, utils
  • Suggests: TreePar
  • Extends:

Authors