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Workshop: Reproducible Research for Teams with GitHub

UC Davis DataLab

Winter 2022

Common links:

Protocols:

The course reader is a live webpage, hosted through GitHub, where you can enter curriculum content and post it to a public-facing site for learners. Supplementary examples for other readings are also appropriate, but please refrain from using it as a space to host slides.

To make alterations to the reader:

  1. Clone this repo.
  2. Edit one of the existing chapter .Rmd files or create a new one. The chapter files are at the top level of the repository. They follow the naming scheme ##_topic-of-chapter.Rmd (an exception to this naming scheme is index.Rmd, which contains the reader's index page). You should enter your text, links, and any supporting media directly into the file.
  3. Run the script gen_html.R to regenerate the HTML files in the docs/ directory. You can do this in the shell with ./gen_html.R or in R with source("gen_html.R").
  4. Once you have made your changes, commit and push both the files you edited and the docs/ directory. The live web page will update accordingly.

Follow the established style and formatting conventions in chapter files, including those for linking to media on the ds.lib server. On the ds.lib server, the course media directory is in the public-facing portion of the DataLab website (ds.lib.ucdavis.edu).

Summary of important files:

  • docs -- output HTML files
  • img -- image files used in chapters
  • _bookdown.yml -- bookdown settings (mostly where files are)
  • _common.R -- R code to run at beginning of R session for each chapter
  • gen_html.R -- R script to generate the HTML files
  • index.Rmd -- index page
  • _output.yml -- bookdown settings (mostly formatting)

License:

CC BY-NC 2.0