What I love about my workflow is that using tools to make my research open and transparent makes my research faster and better! The key pieces that contribute to improving speed and research rigor are 1) rmarkdown (text and R code all in the same document), 2) GitHub (version tracking with automated track changes), and 3) Peer Community In Ecology where I submit my preregistrations (study plan) for peer review before I collect the data.
I write my preregistrations in rmarkdown, which is amazing because I just open this one document in RStudio and everything I need is right there! I don’t have to go looking for which version of the Word document is the latest, I don’t need to search for the various bits of R code that are in a different folder and in several files. Any time I need to update this document (which I do a lot), I just push it to GitHub (with the click of a button in RStudio) and it updates the version automatically and adds my changes to the file’s history, which I can look at any time (and so can anyone else because my GitHub repository is public). My collaborators, staff, and students can do this as well and we can all edit the same file at the same time – GitHub automatically merges our changes into a fully integrated up-to-date version with everyone’s changes tracked. Each preregistration is one rmarkdown document, and it is a living document because as I progress through collecting and analyzing data, I just add the results and discussion sections and flesh out the introductory text and it becomes the final manuscript! I have saved immeasurable amounts of time from doing my science this way.
I submit my preregistrations for pre-study peer review to Peer Community In Ecology (PCI Ecology, https://ecology.peercommunityin.org) because, hey, if I’m going to have my research peer reviewed anyway, I might as well do it before I’ve collected the data so I can give the reviewers and editor a chance to offer methodological changes in case they catch something I didn’t. It saves tons of resources and time by catching these things before the research actually happens! As an editor and reviewer, I have unfortunately had to reject many manuscripts because the methods were not sufficient to answer their question of interest. It is really sad for everyone and could have been prevented if the peer review happened before the study was conducted. After my preregistrations pass peer review at PCI Ecology (they agree to accept the final manuscript as long as I follow my plan), I conduct the study, analyze the data, and turn the preregistration into a final manuscript. I then submit this back to PCI Ecology for its post-study peer review, which is just a check to make sure I did what I said I was going to do and if there were necessary changes along the way (because science NEVER goes how you expect it to!) that these changes maintained the scientific validity of the research. This process saves tons of time because you don’t have to go journal shopping after your study is over, which can take years just for one article.