RStudio development and package website

Open gsim.Rproj in RStudio. The Build pane uses devtools for package installation, checking and roxygen documentation, as in qgg/gact. Edit roxygen comments in R/ and use Build > Document to regenerate help. Edit README.Rmd, then use its Knit button to update README.md. Install devtools and roxygen2 as developer tools if they are missing. Package checks retain the scope and prerequisites documented in AGENTS.md.

Build the website

Website development uses pkgdown, knitr and rmarkdown. Install these developer tools once if missing; RStudio supplies Pandoc. They are not runtime package dependencies. From the project root, run in the RStudio R console:

pkgdown::build_site(examples = FALSE, install = FALSE)

Examples remain display-only. No package installation, simulation, benchmark or biological download is performed by this command. Output goes to ignored website/_site/; existing scientific sources in docs/ are preserved. The pkgdown configuration is _pkgdown.yml. The homepage is README.md, function reference comes from man/, and website-only articles live under vignettes/articles/. Their small include chunks read the authoritative Markdown and adapt links; scientific code is never executed. Edit the original Markdown, not copies or generated HTML. Static downloads in pkgdown/assets/files/ retain the example and notice files; refresh those copies when their authoritative inst/ files change. Article wrappers are excluded from R source packages, so documentation tools are not installation requirements.

For command-line builds, use Rscript with the same expression. RStudio users do not need a custom build.py or build.R, Python or Quarto.

GitHub Pages

Every push to main automatically builds and publishes the website through .github/workflows/pages.yml. Edit in RStudio, Knit README.Rmd when it changes, then commit and push. Local website previews are optional. The workflow prepares R website tools and Pandoc, renders without installing the package or running examples, and uploads only website/_site/.

In repository Settings > Pages, select GitHub Actions. The Publish documentation workflow also retains Run workflow for a manual rebuild on main. Environment protection rules, if configured in GitHub, still apply to deployment. The configured URL is https://psoerensen.github.io/gsim/. A successful Actions deployment establishes that the published site is available.

Authoritative source