A workflow and set of functions to clean your taxonomy data using R.
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README.md

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taxonomyCleanr

The taxonomyCleanr is a user friendly workflow and collection of functions to help you:

  1. Identify and correct misspelled taxa
  2. Resolve taxa to an authority (e.g. Integrated Taxonomic Information System (ITIS))
  3. Get hierarchical rank values
  4. Get common names
  5. Render taxonomic information in the Ecological Metadata Language (EML).

The taxonomyCleanr is based on the taxize R package developed by Chamberlain et al. (2016).

Getting started

R package

Install taxonomyCleanr from GitHub

# Install and load devtools
install.packages("devtools")
library(devtools)

# Install and load taxonomyCleanr
install_github("EDIorg/taxonomyCleanr")
library(taxonomyCleanr)

Documenation

A demonstration of the taxonomyCleanr

Contributing

We welcome contributions of all forms including bug reports, requests for development, and new functionality. Please reference our code conduct and contributing guidelines for submitting pull requests.

Testing

Unit tests are found under /tests and follow the testthat methodology.

Versioning

Versioning for the taxonomyCleanr follows semantic versioning.

Authors

See the list of contributors to this project.