mantaspanos / intro-curriculum-r

Custom curriculum for teaching R, the Unix Shell, & Git with an integrated workflow and reproducible research practices.

U-M Carpentries R Curriculum

This is the custom curriculum developed by the University of Michigan Software Carpentry instance. It is in the beta stage of development; we are continuing to host workshops to gather feedback and polish the curriculum.

The rendered website can be found here.

Repo Layout

1. Top level files

   • index.md - The home page.
   • reference.md - Reference for learners.
   • setup.md - Setup instructions for learners.
   • AUTHORS - Plain text list of the lesson authors.
   • CITATION - Plain text citation instructions.

2. Lesson episodes

   • _episodes/ - Source files in markdown. Episode order is determined by the filename.
   • _episodes_rmd/ - Source files in R Markdown. A lesson should be written in one or the other markdown style, not both. To convert R Markdown files to markdown episodes, run make lesson-rmd.

   Run make lesson-check at any time to check that the lesson files follow the formatting rules

3. Figures are stored in fig/, data sets in data/, source code in code/, and miscellaneous files in files/.

4. _extras/

   • about.md - General notes about the curriculum.
   • discussion.md - For learners who would like to learn more.
   • guide.md - The instructor's guide for the curriculum.
   • bonus_exercises.md - Bonus exercises for learners who want to practice more.

Rendering R Markdown episodes

To render all episodes in _episodes_rmd/, run:

make site

This will create markdown files in _episodes/ for GitHub Pages.

To render just one episode, e.g. _episodes_rmd/01-r-plotting.Rmd, run:

make _episodes/01-r-plotting.md

Workshop Schedule

For a typical 2-day workshop. Can be modified for different workshop formats.

	Title	Source File
Day 1
09:00	Welcome to the workshop	_episodes/00-intro.md
09:15	R for Plotting	_episodes_rmd/01-r-plotting.Rmd
10:30	Break
10:45	R for Plotting (Continued)	continuation of 01-r-plotting
12:00	Lunch Break
13:00	The Unix Shell	_episodes/02-unix-shell.md
14:15	Break
14:30	Intro to git & GitHub	_episodes_rmd/03-intro-git-github.md
16:30	Wrap-up Day 1
Day 2
09:00	R for Data Analysis	_episodes_rmd/04-r-data-analysis.Rmd
10:30	Break
10:45	R for Data Analysis (Continued)	continuation of 04-r-data-analysis
12:00	Lunch Break
13:00	Writing Reports with R Markdown	_episodes_rmd/05-r-markdown.Rmd
14:30	Break
14:45	Writing Reports with R Markdown (Continued)	at end of 05-r-markdown
16:00	Conclusions & Wrap-up	_episodes/06-conclusion.md
16:15	Exit Survey
16:30	End

Helpful links

• How to format lesson files: https://carpentries.github.io/lesson-example/04-formatting/index.html
• Additional instructions for formatting R Markdown lesson files: https://carpentries.github.io/lesson-example/05-rmarkdown-example/index.html
• The Carpentries lesson example repo (source files for the above two links): https://github.com/carpentries/lesson-example
• Already-established SWC curricula: https://github.com/swcarpentry/swcarpentry#lesson-repositories
• Lesson style guide: https://carpentries.github.io/lesson-example/06-style-guide/index.html
• Guide to contributing with git and GitHub: https://github.com/dmgt/swc_github_flow/blob/master/for_novice_contributors.md#

Citation

If you would like to cite our work, please use:

Lapp et al., (2022). Developing and deploying an integrated workshop 
curriculum teaching computational skills for reproducible research. 
Journal of Open Source Education, 5(47), 144, https://doi.org/10.21105/jose.00144

Here's a bibtex entry for LaTeX users:

@article{lapp_developing_2022,
  doi = {10.21105/jose.00144},
  url = {https://doi.org/10.21105/jose.00144},
  year = {2022},
  publisher = {The Open Journal},
  volume = {5},
  number = {47},
  pages = {144},
  author = {Zena Lapp and Kelly Sovacool and Nick Lesniak and Dana King and Catherine Barnier and Matthew Flickinger and Jule Krüger and Courtney Armour and Maya Lapp and Jason Tallant and Rucheng Diao and Morgan Oneka and Sarah Tomkovich and Jacqueline Anderson and Sarah Lucas and Patrick Schloss},
  title = {Developing and deploying an integrated workshop curriculum teaching computational skills for reproducible research},
  journal = {Journal of Open Source Education}
}