diff --git a/README.md b/README.md index 52f4cb6..537fdb9 100644 --- a/README.md +++ b/README.md @@ -1165,6 +1165,8 @@ etc. ### Documentation +#### R package documentation + - https://pkgdown.r-lib.org/index.html - With `pkgdown` you can include in a webpage the reference manual and the vignettes of your package, along with any further custom pages. Don't forget to use bootstrap 5, @@ -1177,6 +1179,40 @@ etc. `pkgdown` pages is possible by Bootstrap 5 paramaters, in this page you find a list of them. These you can put in `_pkgdown.yml` under the `bslib` key. +- See [here](https://github.com/saezlab/ocean/blob/93ecb59506e2cbeb0e77b4c12d42ea3b9cb0124e/.github/workflows/pkgdown.yaml) + how to automate `pkgdown` page build and deployment with GitHub Actions. + You can create such an action manually, or by `use_pkgdown_github_pages` + from the `usethis` package. Check out also + [`_pokgdown.yml`](https://github.com/saezlab/ocean/blob/93ecb59506e2cbeb0e77b4c12d42ea3b9cb0124e/pkgdown/_pkgdown.yml) + and + [`extra.css`](https://github.com/saezlab/ocean/blob/93ecb59506e2cbeb0e77b4c12d42ea3b9cb0124e/pkgdown/extra.css) + in the above repo for more good examples. + +#### R analysis documentation + +- https://workflowr.github.io/workflowr/ - `workflowr` is a `pkgdown` wrapper + for analysis projects. Its main advantage is the nice presentation: the + analysis is presented as a good looking web page. It also offers entry + points to organize the project and re-run specific sections of the + pipeline. It presents git history on the analysis webpage, and notifies + if some parts of the presented results are outdated. A disadvantage is + that it doesn't follow the R package layout, making difficult the use + of many other tools. + +### Reproducibility + +#### R + +- https://rstudio.github.io/renv/articles/renv.html - `renv` is a dependency + management tool for R. In your scripts use the `package::function` + notation or use `library()` calls. When you're about to submit your + analysis, run `renv::init` (later for updating use `renv::snapshot`). + Include the `renv.lock` file in your repo, so anyone who wants to reproduce + your analysis will be able to use all the required packages with the exact + same versions that worked for you. +- https://workflowr.github.io/workflowr/ - `workflowr` is also related to + reproducibility, see details above in the + [documentation](#r-analysis-documentation) section. ## Performance