Practical R Workflow Workshop for NMFS Scientists

Eli Holmes from the Northwest Center hosted an 8-part Practical R Workflow workshop series. The series focused on tools and practices for NMFS scientists to help you be faster, more efficient, and organized in your coding and merging reports with code.

Topics covered

Topic Description
Introduction to workflow using RStudio and Git/GitHub The session video will be posted June 2nd but the link has my lectures notes and short videos of the skills.
More Git/Github The 3 key Git skills. These 3 basic skills are all you need for 95% of your work with Git repositories.
Key Git/GitHub skills We’ll learn how to use issues and releases on GitHub to be more efficient either working alone or in a team. I’ll show you how I use organizations to organize my repositories and some of the nice ‘landing page’ features of GitHub. For those curious about GitHub Actions, I give you a short demo on that too.
Rmarkdown for reports Let’s make a report that updates when our data change and post that to GitHub.
Making plots with ggplot2 Learning ggplot2 will make it much easier to make plots from the big and complex datasets that you deal with on a daily basis.
Intro to R packages How to build an R package in RStudio. In the second half of the lecture, I will show you how to make an R data package and what that can do to allow data documentation, data revision tracking, data versioning and data sharing.
Roxygen2 and pkgdown Even if you don’t do the coding on your team, you should be aware of how documentation works so you can contribute and the tools for automating tasks like a project website so your team doesn’t fall into inefficient workflows.
Advanced Topics for Developers How to set up a NAMESPACE, passing R CMD check, debugging tools, coding GitHub Actions workflows, C++ code in your package. I am going to pass on tips to help you understand how these things work so you don’t waste hours figuring it out or fall back on hacky solutions.