MrFlick / 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#