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Contributing to univariateML development

Source: CONTRIBUTING.md

The goal of this guide is to facilitate contributing to univariateML as quickly as possible. The guide is divided into two main pieces:

  1. Filing a bug report or feature request in an issue.
  2. Suggesting a change via a pull request.

Please note that univariateML is released with a Contributor Code of Conduct (found in CODE_OF_CONDUCT.md). By contributing to this project, you agree to abide by its terms.

Issues

When filing an issue, the most important thing is to include a minimal reproducible example so that we can quickly verify the problem, and then figure out how to fix it. There are three things you need to include to make your example reproducible: required packages, data, and code.

  1. Packages should be loaded at the top of the script, so it’s easy to see which ones the example needs.

  2. Make sure any potential data is easily available to us when we verify your issue.

  3. Spend a little bit of time ensuring that your code is easy for others to read:

    • make sure you’ve used spaces and your variable names are concise, but informative

    • use comments to indicate where your problem lies

    • do your best to remove everything that is not related to the problem.
      The shorter your code is, the easier it is to understand.

    • follow the tidyverse style.

You can check you have actually made a reproducible example by starting up a fresh R session and pasting your script in.

(Unless you’ve been specifically asked for it, please don’t include the output of sessionInfo().)

If you miss a particular estimator, make an issue explaining why its implementation should be prioritized.

Pull requests

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

  1. Create a branch in git and make your changes.
  2. Push branch to github and issue 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 univariateML.

Each of these steps are described in more detail below. This might feel overwhelming the first time you get set up, but it gets easier with practice.

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 seven point checklist:

  1. Motivation. Your pull request should clearly and concisely motivate the need for change.

  2. 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.

  3. Use the tidyverse coding style. Please follow the tidyverse style with camel case allowed for the ml*** functions. Maintaining a consistent style across the whole code base makes it much easier to jump into the code. If you’re modifying existing univariateML code that doesn’t follow the style guide, a separate pull request to fix the style would be greatly appreciated.

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

  5. If fixing a bug or adding a new feature to a function, please add a testthat unit test.

  6. If you wish to provide a new maximum likelihood estimator please read the Implementing New Densities section below.

  7. Make better algorithms for maximum likelihood estimation if you can but please prepared to document the superiority of your new implementation.

This seems like a lot of work but don’t worry if your pull request isn’t perfect. It’s a learning process and members of the univariateML team will be on hand to help you out. A pull request (“PR”) is a process, and unless you’ve submitted a few in the past it’s unlikely that your pull request will be accepted as is. All PRs require review and approval from at least one member of the univariateML development team before merge.

Finally, remember that univariateML is an in-development package. We honorably welcome pull requests and contributions.

Implementing New Densities

  1. Make sure there is a CRAN package containing at least the density function. That is, package::dyourdensity is possible to import. If this does not exist your pull request won’t be accepted.

  2. Search the literature and try to find algorithms. Try to program a fast and reliable algorithm. If you fail to find good custom algorithms, use nlm, constrOptim or something similar. This is the approach taken in mlcauchy and mllogis. mlbeta also uses nlm but does so intelligently and is much faster than mlcauchy and mllogit.

  3. Program an ml*** function following the pattern already established by the other ml*** functions. In particular, be sure to return the correct kind of object, be sure to test for na and numbers out of bounds, and try to make a fast variant of of logLik attribute.

  4. Add tests. There are plenty of patterns in the test_that directory. Be sure to test different kinds of options if applicable (see e.g. mlbeta). You must have 100% code coverage; run covr::report(). Please make more tests rather than fewer.

  5. If the distribution has some strange behavior, such as mllomax has, add the appropriate section to the distributions vignette.

  6. Make a pull request!

Acknowledgements

This file is a lightly modified version of CONTRIBUTE.md of the R package cvcqv available here.