Update wiki/paper

Coalesce the Wiki into a coherent document that can be generated via a vignette, and which serves as a blueprint of a potential paper (which obviously needs to be a drastically shortened version).

Points to address in a paper:

* [ ] Reproducibility (Jupyter, RMarkdown …) vs reusability
* [ ] Code modularisation
* [ ] Typing and use of NSE

Start by reading the existing Wiki and determining how its content should be organized into a vignette. Use the checklist as the acceptance criteria: cover reproducibility versus reusability, code modularisation, and typing and NSE, while producing a coherent document that can serve as a shortened paper blueprint.

Written by the indexing model from the issue text.