Is rhdf5 the best library? I understand there is ncdf4 and h5r, and rgdal. I understood that R support for HDF5 was limited so I have not used R much for this purpose.
I don't think R support for HDF5 is "limited," I think it's just poorly implemented in a few ways (another is that you need a separate package to get 64-bit integer support, which is another problem with R in general).