Contributing to latentcor

Contributions to latentcor follow the same principles as stated in the guideline for contributors to the tidyverse ecosystem of R (see here for more details: development contributing guide ).

Fixing typos

You can refer to this for proposing changes with pull request from a fork. You can fix typos, spelling mistakes, or grammatical errors in the documentation directly using the GitHub web interface, as long as the changes are made in the source file.

If you find any typos in an .Rd file, then please make changes in the corresponding .R file, as .Rd files are automatically generated by roxygen2 and should not be edited by hand.

Bigger changes

The first step here for you to make any changes is to install devtools using install.packages("devtools"). If you want to make a bigger change, it’s a good idea to first file an issue and make sure someone from the team agrees that it is needed. If you have found a bug, please file an issue that illustrates the bug with a minimal reproducible example, a reprex (this will also help you write a unit test, if needed).

Pull request process

To contribute a change to latentcor, you follow these steps:

  1. Create a branch in git, give it a descriptive name, and make your changes.
  2. Push branch to GitHub and issue a pull request (PR).
  3. Discuss the pull request.
  4. Iterate until either we accept the PR or decide that it’s not a good fit for latentcor.

If you’re not familiar with git or GitHub, please start by reading http://r-pkgs.had.co.nz/git.html

Pull requests will be evaluated against a checklist:

  1. Motivation. Your pull request should clearly and concisely motivate the need for change. Please describe the problem your PR addresses and show how your pull request solves it as concisely as possible.

Also, include this motivation in NEWS so that when a new release of latentcor comes out it’s easy for users to see what has changed. Add your item at the top of the file and use markdown for formatting. The news item should end with (@yourGithubUsername, #the_issue_number).

  1. Only related changes. Before you submit your pull request, please check to make sure that you haven’t accidentally included any unrelated changes. These make it harder to see exactly what’s changed, and to evaluate any unexpected side effects.

Each PR corresponds to a git branch, so if you expect to submit multiple changes make sure to create multiple branches. If you have multiple changes that depend on each other, start with the first one and don’t submit any others until the first one has been processed.

  1. Use latentcor coding style. We tried to adhere as closely as possible to the official tidyverse style guide – please do so as well. Maintaining a consistent style across the whole code base makes it much easier to jump into the code. If you’re modifying existing latentcor code that doesn’t follow the style guide, a separate pull request to fix the style would be greatly appreciated.

  2. If you’re adding new parameters or a new function, you’ll also need to document them with roxygen2. Make sure to re-run devtools::document() on the code before submitting.