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Contributing to CyneRgy

J. Kyle Wathen

September 17, 2026

ContributingToCyneRgy.Rmd

If you would like to contribute to CyneRgy there are multiple avenues to get involved.

You can submit an issue, report a bug, or add your own functionality and examples for others to learn from. To add examples, please follow the instructions below.

Style Guide

Please follow the Biopharm Soft style guide when developing code so that the style is consistent across different developers.

Adding an Example

To make sure the examples are clear and included in the package website please use the following steps. These steps are changing over time so if you find something that is not clear or incorrect, please add an issue.

  1. Use Git to clone the CyneRgy repository.
  2. If an issue does not exist in the CyneRgy repository, then please add one and use it to create a new branch for development. If an issue already exists, then create a branch for development.
  3. Start a new example with CyneRgy::CreateCyneRgyExample().
  4. Place the completed example in inst/Examples; keep its example-specific functions there rather than in the package-level R directory.
  5. Use Git to add the files to the repository.
  6. Update the vignettes/ExampleOutline.Rmd file to include a brief description and link to the new example.
  7. Use Git to commit to the branch created above.
  8. Add a Pull Request in GitHub to merge your development branch to the Dev branch.

Please note that all branches are merged into Dev. Dev is used to combine all branches, then a branch is created for building the package website and reviewed for documentation and completeness. Once this is done, the Dev branch is merged into Main via a Pull Request from the repository owner, and the example is then included on the website as well as in the package when it is installed from GitHub.

Package Development

This document is intended to help with development of this package.

After changing package code or documentation, run devtools::document(), devtools::test(), devtools::check(), and pkgdown::build_site(). Include the relevant generated files under man/ and docs/ in the pull request.

Helpful packages

  1. pkgdown - Package used to create the package website.
usethis::use_pkgdown_github_pages()  # Likely you do not need to run this again as it was set up already.
devtools::document() # Build the Rd scripts in /man for the reference section using the R scripts in /R.
devtools::install() # Re-install CyneRgy after adding new functions to /R.
pkgdown::build_site() # Build the site pages using Rmd scripts in /vignettes. Preview the site locally before publishing.
  1. testthat - Useful for creating and testing R packages.
  2. covr - Use to create a test coverage report with the following commands
usethis::use_coverage()  # Likely you do not need to run this again as it was set up already.
covr::package_coverage() # Computes the coverage
covr::report()           # Creates a report
  1. Git for Windows - Git for Windows; I believe you need to install this to use source control from Windows.
  2. Tortoise Git - Free Windows shell program (runs in Windows explorer by right-clicking on a folder/file). This allows you to commit changes to GitHub without having to remember all the commands.
  3. GitHub Flow - Helps understanding GitHub flow.
  4. Getting Started with Source Control - An introduction to source control and getting started with Git.
  5. Git Tutorial - Useful Git tutorial.

Helpful Code Snippets

If you need help please ask Kyle Wathen or another team member.

Add a code snippet by selecting Tools → Global Options → Code → Edit Snippets. In the Snippets menu, choose R. When creating new snippets, the keyword “snippet” should start in column 1 and the snippets should be indented. To insert a snippet in RStudio, type the snippet name, or partial name, and press Tab.

Snippet to insert a new comment (newcom) will insert a commented code block.

snippet newcom
   #################################################################################################### .
   # ${0} ####
   #################################################################################################### .

Snippet to insert a header (header).

snippet header
   #################################################################################################### .
   #   Program/Function Name: ${1}
   #   Author: J. Kyle Wathen
   #   Description:
   #   Change History:
   #   Last Modified Date:
   #################################################################################################### .