Week 3: Workflow and RMarkdown
We want to work seamlessly, painlessly, and in such a way that you can easily find code and data many years after completing a project.
This week, we will cover RMarkdown - a language that allows integration of text and R code. We will also cover best-practices in arranging project folders.
Lecture Topics
- What is workflow?
- Using RProjects to organize workflow
- Best practices in arranging project folders
- Minimal Reporducible Examples
- Introduction to RMarkdown
- Introduction to Version Control (concept only)
Resources
- R Studio Cheat Sheets
- Bookdown: Authoring books and technical documents with R Markdown
- Designing Projects: Nice R Code
- Minimal Reproducible Examples
- Minimal Reproducible Examples 2
- Reprex package
- Math notation in Markdown
- Markdown in Microsoft Teams
If you’re interested in using GitHub, I also draw your attention to the folowing resources:
- Excuse me, do you have a moment to talk about version control?
- Version control - Intro to Git for Biologists
- Happy Git and GitHub for the useR
Code and Data
Going forward, I will include a project file for most weeks, enclosed in a .zip file. Please download the .zip file and unzip it before class starts.
A sample template for 6002’s major assignment. We will be building this in class - use this if you get stuck.
Our Minimal Reproducible Activity file is here:
And if you want to see solutions to it:
Lecture slides
Slides available via speakerdeck