I have an R package that uses roxygen2. It has some C code in /src, and I have just started working with Doxygen. Are there any ways to combine the documentation or integrate compiling with roxygen2? Any "best practices" for where to put the C code documentation?
Googling for roxygen2 and doxygen primarily leads to roxygen is similar to doxygen results. I have found a few packages with Doxyfiles, but no consistent organization. For example, lme4 has inst/doc/Doxyfile output to a folder called doxygen outside the lme4 source directory. There is also a Doxyfile in the root directory of the Matrix (but in previous releases was in inst. This documentation is also exported outside the package directory.
Is there any reason not to include the C documentation inside a package, or why is Doxygen so infrequently used within R packages, despite widespread use of C?
update: see related roxygen2 feature request