# treebase 0.0-6

Interface to the API for TreeBASE

# treebase

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

- Development version source code on github
- HTML package documentation
- Report issues, bugs or feature requests

## 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