Contributing Guidelines

git structure

The active branch is development. development is merged into main for releases. Please submit your pull requests to development.

Repository structure

This repository is structured as a standard R package following the conventions outlined in the Writing R extensions manual. A few additional files are provided that are not part of the built R package and are listed in .Rbuildignore, such as .travis.yml, which is used for continuous testing and integration.


All code for this package is found in R/. All functions should be thoroughly documented with roxygen2 notation; see Documentation. Code should conform to the rOpenSci Style guide.


Any new feature or bug-fix should include a unit-test demonstrating the change. Unit tests follow the testthat framework with files in tests/testthat. Please make sure that the testing suite passes before issuing a pull request. This can be done by running check() from the devtools package, which will also check for consistent documentation, etc.

This package uses the travis continuous testing mechanism for R to ensure that the test suite is run on each push to Github. An icon at the top of the indicates whether or not the tests are currently passing.


All of the function documentation is generated automatically. Please do not edit any of the documentation files in man/ or the NAMESPACE. Instead, construct the appropriate roxygen2 documentation in the function files in R/ themselves. The documentation is then generated by running the document() function from the devtools package. Please consult the Advanced R programming guide if this workflow is unfamiliar to you. Note that functions should include examples in the documentation. Please use \dontrun for examples that take more than a few seconds to execute or require an internet connection.

Likewise, the file in the base directory should not be edited directly. This file is created automatically from code that runs the examples shown, helping to ensure that they are functioning as advertised and consistent with the package README vignette. Instead, edit the README.Rmd source file in manuscripts and run make to build the README.

General Development Goals & Guidelines

  1. High-level functions to align taxa to authority systems with little to no knowledge about the data (i.e. name matching).
  2. Errors and warnings should guide users to solutions.


These contributing guidelines are based on those of the rOpenSci EML project.

EDIorg/taxonomyCleanr documentation built on March 17, 2023, 11:22 a.m.