The trial-by-trial behavioral adaptation project was larger than my two previous research projects and introduced several new challenges in organizing the analysis. I followed the planned minimalist repository structure and kept the project organized throughout development. As the analysis became more complex, however, I found that the same structure became increasingly difficult to navigate and review.
The main problem appeared after the modeling, in visualizing and exporting the results. I had three main notebooks, supported by R scripts, including a data inspection notebook, an exploratory data analysis notebook, and a modeling notebook. I used this structure throughout the project as I had planned. As a result, the modeling notebook and the models R script contained the code for exporting the final results. This did not create a reproducibility problem, but the larger files became harder to review and navigate.
A repository structure that works well for a small project may not scale effectively to a larger analysis. Simplicity is valuable, but the structure should also make distinct stages of an analysis easy to locate, review, and maintain. Separating final result generation into a dedicated notebook and script would have improved the organization of the final stages without substantially increasing the complexity of the repository.
By considering the size and complexity of the project when designing the repository structure, I will try to keep the structure as simple as possible, but also use additional notebooks and scripts when they improve organization, review, and reproducibility.