32  R Markdown workflow

Earlier, we discussed a basic workflow for capturing your R code where you work interactively in the console, then capture what works in the script editor. R Markdown brings together the console and the script editor, blurring the lines between interactive exploration and long-term code capture. You can rapidly iterate within a chunk, editing and re-executing with Cmd/Ctrl + Shift + Enter. When you’re happy, you move on and start a new chunk.

R Markdown is also important because it so tightly integrates prose and code. This makes it a great analysis notebook because it lets you develop code and record your thoughts. An analysis notebook shares many of the same goals as a classic lab notebook in the physical sciences. It:

Much of the good advice about using lab notebooks effectively can also be translated to analysis notebooks. We’ve drawn on our own experiences and Colin Purrington’s advice on lab notebooks (https://colinpurrington.com/tips/lab-notebooks) to come up with the following tips: