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.

1. 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

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

2. _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/swcgithubflow/blob/master/fornovicecontributors.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:

bib @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} }