Contributing
Source:CONTRIBUTING.md
Welcome! Happy to have you here. Thank you in advance for your contribution and interest in epocakir.
Prerequisites
epocakir is written in pure R. You’ll need the R>=4.0 and dev packages. Currently R Tools is not required.
install.packages(c("devtools", "roxygen2", "lintr", "styler", "testthat", "knitr"))Project Structure
epocakir is a standard, single R package with R code in the R/ directory, data in the data/ directory and testing using testthat.
epocakir/
├── .github/ # GitHub Actions
├── R/ # R source code
│ ├── aki.R
│ ├── ...
│
├── data/ # .rda Data files
│ ├── aki_pt_data.rda
│ ├── ...
│
├── data-raw/ # Data origin
│ ├── aki-data.R
│ ├── ...
│
├── man/ # Docs auto-generated with roxygen
│ ├── aki_bCr.Rd
│ ├── ...
│
├── tests/ # Testing
│ ├── testthat.R
│ └── testthat
│ ├── test-aki.R
│ ├── ...
│
├── cran-comments.md # CRAN submission comments
├── DESCRIPTION # Package metadata
├── NAMESPACE # Auto-generated with roxygen
├── README.Rmd # Package README
├── README.md # Auto-generated with knitr
├── ...Development
Running Tests
If you’re using RStudio, press Cmd/Ctrl + Shift + T (or run devtools::test() if not) to run all the tests in a package.
devtools::test()
#> ℹ Testing epocakir
#> ✔ | F W S OK | Context
#> ✔ | 24 | aki
#> ✔ | 6 | anemia
#> ✔ | 529 | ckd [1.0s]
#> ✔ | 44 | utils
#>
#> ══ Results ════════════════════════════
#> Duration: 2.1 s
#>
#> [ FAIL 0 | WARN 0 | SKIP 0 | PASS 603 ]Documentation
Adding Documentation
Documentation is generated from the source code using roxygen2. To add documentation to a function, add a comment block above the function.
Building Documentation
To build the documentation, run the following command in the R console:
devtools::document()To build the pkgdown website run the following command in the R console:
pkgdown::build_site()Release
Preparing for Release
Set up a GitHub personal access token for the repository and create a GitHub issue with a checklist. Run through the checks as required, and additional ones below:
# Creat new GitHub issue
usethis::use_release_issue()
# Run additional checks
devtools::spell_check()
urlchecker::url_check()
rhub::check_for_cran()
rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
revdepcheck::revdep_check(num_workers = 4)
devtools::check_rhub()
devtools::check_mac_release()
devtools::check_win_devel()