Practical R Workflow for Scientists Summer 2020
These short sessions (45min to 1hr) will be focused on tools and practices for NMFS scientists to help you be faster, more efficient and organized in your coding and in merging reports with code. The focus of these workshops is practical skills and tools. Each session will be stand-alone. While the sessions will be introductory, I will give you links to my GitHub repositories that illustrate more complex examples (and that you can copy and build on).
Target audience: You already code in R, maybe use RStudio too, but want to learn some tips about being more efficient from a seasoned NWFSC R programmer who does the kind of coding and work that you do.
About me: I am a modeler/applied mathematician and I am immersed in R. I develop R packages for public use. I teach time-series analysis at the University of Washington (using R) and I teach workshops on R and reproducible research.
Topics
Week 1. Introduction to workflow using RStudio and Git/GitHub/GitLab Video
Week 2. More Git/GitHub/GitLab + Basic coding practices for reproducible and extendible code Video
Week 3. Rmarkdown for reports: how to do big tables and export formats for Word docs Video
Week 5. Part 2. Documenting your code and data with Roxygen Video
Unfortunately at about 40min in, I managed to corrupt my R packages and could not demo any more so covered the material verbally. The problem demonstrates why I try to have few dependencies in my packages! One of the dependencies in my SardineForecast package had an install problem and corrupted the pkgload package.
Week 6. Part 3. Vignettes and plot/print methods for your package. Video
Week 7. More Git. Merge conflicts, branches, and reverting changes. Video
Week 9. Introduction to Tidyverse verbs.
NWFSC Math Bio Program