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An Interface to the Open Tree of Life API

Source: R/rotl-package.R
rotl.Rd

The Open Tree of Life is an NSF funded project that is generating an online, comprehensive phylogenetic tree for 1.8 million species. rotl provides an interface that allows you to query and retrieve the parts of the tree of life that is of interest to you.

Details

rotl provides function to most of the end points the API provides. The documentation of the API is available at: https://github.com/OpenTreeOfLife/opentree/wiki/Open-Tree-of-Life-APIs

Customizing API calls

All functions that use API end points can take 2 arguments to customize the API call and are passed as ... arguments.

  • otl_v This argument controls which version of the API your call is using. The default value for this argument is a call to the non-exported function otl_version() which returns the current version of the Open Tree of Life APIs (v2).

  • dev_url This argument controls whether to use the development version of the API. By default, dev_url is set to FALSE, using dev_url = TRUE in your function calls will use the development version.

For example, to use the development version of the API, you could use: tnrs_match_names("anas", dev_url=TRUE)

Additional arguments can also be passed to the GET and POST methods.

Acknowledgments

This package was started during the Open Tree of Life Hackathon organized by the OpenTree of Life, the NESCent Hackathon Interoperability Phylogenetic group, and Arbor.