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Contributing to restrictedROC

This outlines how to propose a change to restrictedROC. For a detailed discussion on contributing to this and other tidyverse packages, please see the development contributing guide and our code review principles.

Fixing typos

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. This generally means you’ll need to edit roxygen2 comments in an .R, not a .Rd file. You can find the .R file that generates the .Rd by reading the comment in the first line.

Bigger changes

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’s needed. If you’ve found a bug, please file an issue that illustrates the bug with a minimal reprex (this will also help you write a unit test, if needed). See our guide on how to create a great issue for more advice.

Pull request process

  • Fork the package and clone onto your computer. If you haven’t done this before, we recommend using usethis::create_from_github("ggrlab/restrictedROC", fork = TRUE).

  • Install all development dependencies with devtools::install_dev_deps(), and then make sure the package passes R CMD check by running devtools::check(). If R CMD check doesn’t pass cleanly, it’s a good idea to ask for help before continuing.

  • Create a Git branch for your pull request (PR). We recommend using usethis::pr_init("brief-description-of-change").

  • Make your changes, commit to git, and then create a PR by running usethis::pr_push(), and following the prompts in your browser. The title of your PR should briefly describe the change. The body of your PR should contain Fixes #issue-number.

  • For user-facing changes, add a bullet to the top of NEWS.md (i.e. just below the first header). Follow the style described in https://style.tidyverse.org/news.html.

# Use pre-commits to check your code before committing it
remotes::install_github("lorenzwalthert/precommit")
precommit::install_precommit()
precommit::use_precommit()

# Increase the versions, manually or by using usethis::use_version()
usethis::use_version("minor")
usethis::use_version("dev")

# Add new functionality and document it
# During development, have a clean R environment and run devtools::load_all() to load the current status of the package
devtools::load_all()

# After adding new functionality, run devtools::check() to update the documentation
devtools::check()
devtools::document()

# Vignettes are a great way to document your package
# Add a new vignette by running
usethis::use_vignette("vignette_name")
# Change the vignette in vignettes/vignette_name.Rmd
# Build the vignette by running
devtools::build_vignettes() # This also installs the package

# Articles
# Instead of a vignette, you can create an article, which is a term used by
# pkgdown for a vignette-like .Rmd document that is not shipped with the package,
# but that appears only in the website.
usethis::use_article("article_name")


devtools::build_readme() # This updates the README.md file from the README.Rmd


# Further arguments of devtools::build_site() are forwarded to pkgdown::build_site():
# https://pkgdown.r-lib.org/reference/build_site.html
devtools::build_site()
devtools::build_site(devel = TRUE, lazy = TRUE) # Use this for faster iteration during development
  • Disable pre-commit for a single commit: git commit . -m 'quick fix' --no-verify

Code style

  • New code should follow the tidyverse style guide. You can use the styler package to apply these styles, but please don’t restyle code that has nothing to do with your PR.

  • We use roxygen2, with Markdown syntax, for documentation.

  • We use testthat for unit tests. Contributions with test cases included are easier to accept.

Code of Conduct

Please note that the restrictedROC project is released with a Contributor Code of Conduct. By contributing to this project you agree to abide by its terms.

How was this package created?

# for VSCode
install.packages("languageserver")
install.packages("devtools")
usethis::create_tidy_package("/home/gugl/clonedgit/ggrlab/restrictedROC")
usethis::proj_activate("/home/gugl/clonedgit/ggrlab/restrictedROC")
usethis::use_tidy_style(strict = TRUE)
usethis::use_git()

usethis tells you to envoke further github-related commands. There is two ways to continue: 1. Create a personal access token (PAT) and use it to authenticate with github 2. Manually push the package to github

Pushing manually works fine, but some advanced usethis commands won’t work properly, therefore I will continue with the PAT.

usethis::create_github_token()
gitcreds::gitcreds_set() # Then enter the freshly generated token
usethis::use_github(
    organisation = "ggrlab",
    private = FALSE,
    visibility = "public"
)

WARNING!!! If an error occurs because e.g. the repository exists already at github, use the following instead of usethis::use_github():

git branch -M main_devel
git remote add origin git@github.com:ggrlab/restrictedROC.git
git checkout main
git merge main_devel --allow-unrelated-histories
git push -u origin main
git branch --delete main_devel
usethis::use_tidy_github()
usethis::use_tidy_github_actions()
# overwrite tidy's default "check-full" with "check-standard"
# to not run so many checks
usethis::use_github_action("check-standard")
usethis::use_tidy_github_labels()
usethis::use_pkgdown_github_pages()

Additional information:

usethis::use_author(
    given = "Gunther",
    family = "Glehr",
    email = "gunthergl@gmx.net",
    role = c("aut", "cre"),
    comment = c("ORCID" = "0000-0002-1495-9162")
)
usethis::use_lifecycle()
usethis::use_news_md()
lintr::use_lintr(type = "tidyverse")
# Change manually to:
# linters: linters_with_defaults(line_length_linter = line_length_linter(120),indentation_linter = indentation_linter(4)) # see vignette("lintr")
# encoding: "UTF-8"

precommit is a wonderful tool to check your code before committing it.

# https://lorenzwalthert.github.io/precommit/articles/precommit.html
# install.packages("precommit")
# bash::$ conda deactivate
# bash::$ pip3 install pre-commit
precommit::install_precommit()
precommit::use_precommit()

Before committing: pre-commit install --hook-type pre-push, then commit.

Used packages:

usethis::use_package("ggplot2")
usethis::use_package("patchwork")
usethis::use_package("pROC")
usethis::use_package("ggpubr")
usethis::use_package("stats")
usethis::use_package("tibble")
usethis::use_package("dplyr")
usethis::use_package("labeling")
usethis::use_package("tidyr")
usethis::use_package("statmod")
usethis::use_package("future.apply")
usethis::use_package("readxl", type = "Suggests")
usethis::use_package("h2o", type = "Suggests")
usethis::use_package("data.table", type = "Suggests")
precommit::snippet_generate("additional-deps-roxygenize")