In jabenninghoff/rdev: R Development Tools

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R Analysis Packages are an extension of the standard R package layout designed to support publishing a collection of R notebooks used for data analysis as static html, typically using GitHub Pages.

R Notebooks include a YAML header and R Markdown body. The Analysis Package Layout follows the convention that the first non-blank line in the body of an R notebook serves as a brief description of the work. rdev includes an "Analysis Notebook" RStudio R Markdown template (File > New File > Rmarkdown > From Template) and a README.Rmd template optionally installed with use_analysis_package() that dynamically builds a list of notebooks and descriptions when devtools:build_readme() is run.

Starting in version 1.8.0, rdev also supports publishing Analysis Notebooks using Quarto as an alternative to the original use_analysis_package().

rdev versions 1.10.2 and newer also support use of Quarto Documents (.qmd) for Analysis Notebooks, although RStudio currently doesn't support .qmd files as document templates.

The table below documents the complete R Analysis Package layout:

Path: Path to the file or directory relative to the package root
R: Included in the R package definition
g: Stored in git
Function: The function of the file or directory

Path | R | g | Function :------------------------|:--|:--|:----------------------------------------------------------------------------------------------------------------------------------------------------- .Rbuildignore | |x| Files excluded from the package, sorted using sort_rbuildignore() .RData | | | Saved workspace - not used .Rhistory | | | R command history .Rprofile | |x| Used by renv and to attach development tools and set project options .Rproj.user | | | RStudio local project files .git | | | git version control .github | |x| GitHub templates and workflows .gitignore | |x| git exclusions based on GitHub R. Generated files outside of docs (used by GitHub Pages) are excluded. .lintr | |x| lintr configuration as described in the Style Guide, vignette("style-guide") .nojekyll | |x| Disable Jekyll processing on GitHub Pages .quarto | | | Used by Quarto DESCRIPTION |x|x| Package metadata. Use "Suggests" for development tools, per renv LICENSE |x|x| Generated with usethis::use_mit_license() LICENSE.md | |x| See above, used by pkgdown and Quarto NAMESPACE |x|x| Automatically generated with roxygen2 NEWS.md |x|x| Release notes, used by get_release(), pkgdown and Quarto R |x|x| All project functions go here, with roxygen2 comments README.Rmd | |x| Generated with usethis::use_readme_md() or rdev template README.md |x|x| Generated with devtools::build_readme() TODO.md |x|x| To-do list, inspired by renv's historical TODO.md _freeze | |x| Used by the Quarto freeze option _pkgdown.yml | |x| pkgdown metadata, stored in the project root to make it more discoverable (not used with Quarto) _quarto.yml |x|x| Quarto configuration file analysis |x|x| Exploratory data analysis in R Notebooks, R Presentations, and Quarto documents. Include functions from the R directory using library(), not source(). analysis/_metadata.yml |x|x| Quarto directory configuration file analysis/assets |x|x| External assets (images, other files) included in R Notebooks analysis/data |x|x| Used to store small data sets used for analysis and exported data as csv files analysis/import | | | Used for local storage of large data sets analysis/rendered | | | Manually rendered versions of analysis/ files to be included in docs/, like .Rpres files changelog.qmd |x|x| Quarto front-end to NEWS.md demos |x| | Not used, as recommended by R Packages docs | |x| Used by build_analysis_site() and build_quarto_site() to render the R Package and Notebooks for GitHub Pages exec |x| | Command line executable scripts - not used index.qmd |x|x| Quarto home page, using the listing page format inst |x|x| Installed files: templates and WORDLIST inst/bin |x|x| Used for shell scripts that support development, like setup-r inst/rmarkdown/templates |x|x| R Markdown Templates man |x|x| Automatically generated with roxygen2 package.Rproj | |x| Use the same name for the package, .Rproj, directory, and GitHub repository pkgdown | |x| Store all pkgdown files here (not used with Quarto) po |x|x| Used for Internationalization if needed renv | |x| Used by renv renv.lock | |x| renv lockfile tests |x|x| Tests using testthat and spelling tools |x| | Auxiliary files needed for building packages - not used vignettes |x|x| Package vignettes and articles, written in R Markdown