Roxygen2 documentation

[evanbiederstedt]

Hi @teng-gao

It would be nice to get this on CRAN when the code is ready. The big impediment to this is always the roxygen2 documentation.

--- if a function is not exported, please use the tag #' @keywords internal. It's useful to know which functions are exported and which are not
--- if a function is exported, please document all fields. Please use the format #' @parameterName type Explanation here (default=xxx). It's very useful to know the data type in the rxoygen2 comments.
--- it will be useful for CRAN reviews if all exported functions have examples, but....that doesn't always happen. But let's try our best.

With this, the other steps will be much easier, and we can quickly get this on CRAN.

[evanbiederstedt]

To clarify, let's only worry about this once you're ready to publish the package. I'll help clean things up.

Thanks, Evan

[teng-gao]

Will do. I think once the functions are mostly finalized I'll start adding those.

[evanbiederstedt]

@teng-gao
Some requests:

• Convert all R files to use the extension *.R (not *.r)
• All functions either need two tags: #' @export or #' @keywords internal

--- #' @keywords internal is for internal functions, which will be used in the package, but users cannot access them on the command line when library(Numbat). For this package, I would recommend you make most functions internal.
--- #' @export means the functions are exported. You then must document these as we do with other R packages, e.g. https://github.com/kharchenkolab/sccore/blob/main/R/helpers.R#L9-L21 or https://github.com/evanbiederstedt/edlibR/blob/main/R/main.R#L5-L48

You need to invest time in documenting these; it's a high priority. (I realize that writing papers are more important, but science needs robust software which others can use and trust. )

I'll help; slack me

Thanks, Evan

[evanbiederstedt]

We can return to this as we put this package on CRAN. All of this is still relevant CC @teng-gao @hiraksarkar

Refer to that email with Peter