A simple kit to use computational notebooks for more openness, reproducibility, and productivity in research
Fig 2
Schematics of the organization of a research project (proj_name) around a computational notebook (proj_name.Rmd/jl, referring to an RMarkdown or Julia file).
The notebook contains narrative text supplementary to the manuscript’s main text, as well as text explaining the reasoning behind the computational work (included as code blocks) and its respective outputs (either kept on the notebook or saved as figures or tables). The notebook stays at upper level of a file structure (Fig 1), which provides easy access to all relevant folders for input (purple) and output (green) files through relative paths. The gray area shows subfolders that are nested inside folders (e.g., the figures and tables folders are inside the text folder). The notebook, along with all the files in the project’s folder, can be subjected to version control and be referenced in a lab notebook, thanks to the nested structure of the project. We recommend publishing it as your main supplementary material to the manuscript, along with a rendered version (.pdf or.html), any scripts, and not yet public data you use.