Kristina Riemer and Jessica Guo co-taught the first half of the ESA SEEDS Critical Skills workshop during the month of September. The twelve workshop participants learned about collaborating and sharing (shell, git/GitHub), project management and reproducible workflows (RStudio, tidyverse packages) and documentation and publishing (Markdown, RMarkdown). Materials and notes for all workshop lessons are published online and we encourage anyone who teaches this content to help themselves to using and remixing.
We had many deep dives into debugging individual computer issues (with help from Julian Pistorius) and good conversations about making nuanced choices: between forking and cloning, R or RMarkdown, when to split code up and when to lump. The answer, as ecologists often confront, is that it depends. The factors influencing project management and organizational choices often boil down to intent and familiarity.
Open science encourages the practice of science to take place in public view, which often alters the intent of our code. Rather than having to work just once, publicly available code should ideally be easy to read, well-documented, and reproducible. With most journals now requiring data and code archiving as a condition of publication, our workshop intends to help participants practice these principles early and often, rather than scrambling to do so once their papers are accepted. Our future selves will thank us!
We recognize that familiarity is an important limitation to adoption of new practices. Most workshops (including ours) present an overwhelming amount of information; to fully implement all best practices at once is unfeasible and contrary to how anyone learns to build skill. We offer this variety of skills so that learners can adopt what they need most immediately, and have a foundational introduction to other topics for later. Many of us adopt new practices only when absolutely necessary, so we understand completely. It was a pleasure to work with this group of early career ecologists, who rose to the occasion and helped each other. We hope this community of practice continues on Slack, far beyond the extent of the workshop!