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.
Code
All code for this package is found in R/, (except compiled source code, if used, which is in /src). All functions should be thoroughly documented with roxygen2 notation; see Documentation. Code should conform to our Style guide
Testing
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 README.md indicates whether or not the tests are currently passing.
This package also uses codecov.io to measure test coverage. While not all code can be covered by automated tests (in particular, functions involving user prompts), try to avoid decreasing coverage by writing unit tests for any contributed code. Codecov.io will flag PRs that decrease coverage.
Documentation
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 README.md 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.