I appreciate the efforts to make the pipeline used in this study reproducible by providing code organized in a public repository. I do, however, not agree that it is useful to call the collection of scripts found in the repository an R-package. One of the central aims of R-packages is to allow easy installation by listing and automatically installing dependencies. This holds for both packages hosted on one of the community archives (e.g. CRAN) and packages which are not in those archives. The code of the pipeline presented here can't follow these standards as one of its central dependencies is not open source software.

In addition, the R package "build system" enforces certain practices for organization of code an minimal requirements for documentation. These practices are also not followed and the documentation requirements are not met in the pipeline.

I am sure the code is useful for reproducibility of the presented work, but wouldn't it be better to call JAMP what it is: a collection of R scripts?