Rstan_package_skeleton folder roles

Developers
1

Hello, someone with limited overall development experience here, working on their first rstan package. Very early versions of what I’m trying to do are working but I’m realizing that I don’t fully understand the folders that rstan_package_skeleton installs that are not part of the “normal” R package folder structure, namely /inst/include and /tools.

From the rstan developer guidelines (http://mc-stan.org/rstantools/articles/developer-guidelines.html) I gather that /inst/include is meant for code chunks that may get reused and I was pointed to the rstanarms package. From there it seemed like reused stan code chunks are left in /src/stan_files and only re-used c++ code chunks are in /inst/include. Is this impression accurate and if I don’t have c++ code chunks (currently only the blank meta_header.hpp file is there) should I delete /inst for now?

In terms of /tools rstanarm only has the make_cc.R file that rstan_package_skeleton() automatically sets up. It seems like the purpose of the file is to make c++ classes from stan files but that’s all I can tell from reading documentation.

I’m sorry for my novice questions, I was just curious about the roles of these folders and what code I might be writing belongs in them (and no one I’m working with has much more experience than I do). If anyone knows of resources that might solve these types of questions in the future I would be glad to have them!
Thanks for your time

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We changed things up a good bit for Stan 2.17.x and maybe not all of the documentation is current. As of now, /inst/include/ is meant for C++ code that is custom to your R package and there may not be any in your case (but you don’t need to delete anything). Conversely, src/stan_files/chunks is meant for Stan code that gets included in multiple Stan programs that are in the root of src/stan_files. To use this just do something like

#include chunks/license.stan

at the top of your Stan programs.

There is stuff in tools/ that is called when you do R CMD build mypackage and similar. The tools/ folder gets deleted in mypackage_1.0.tar.gz so you don’t need to touch it or even worry about it.

3

Thanks so much for your time, appreciate the work you all do.