We need to move toward having the pre-analysis plan, code, outputs, everything in the same R markdown file or Jupyter notebook.
For Markdown, use knitr to generate the report https://yihui.org/knitr/
For Jupyter, use stitch https://pystitch.github.io/
When knitr or stitch is run, the report can be saved to the reports folder. At that time, the researcher should commit a Version of the Git repository, and then continue revising the main notebook / rmarkdown. This will reduce redundancies while recording provenance of the data, research plan, and code.
We need to move toward having the pre-analysis plan, code, outputs, everything in the same R markdown file or Jupyter notebook. For Markdown, use knitr to generate the report https://yihui.org/knitr/ For Jupyter, use stitch https://pystitch.github.io/
When knitr or stitch is run, the report can be saved to the reports folder. At that time, the researcher should commit a Version of the Git repository, and then continue revising the main notebook / rmarkdown. This will reduce redundancies while recording provenance of the data, research plan, and code.