Removed R-code subdir, and updated index.rst with links.

This contributes to [Issue 211](https://github.com/biom-format/biom-format/issues/211).

https://github.com/biom-format/biom-format/issues/211

This also replaces the previous (failed) [pull request 213](https://github.com/biom-format/biom-format/pull/213)