R CMD check output

[b-steve]

The R CMD check output shows a lot of minor issues. Here's the check log: 00check.log. Ideally we should get this tidied up.

There are a lot of warnings about missing components of documentation. For now, the documentation doesn't have to be perfect, but we should get some brief descriptions of the different arguments so that an informed user has the ability to understand what it does, and so we can write more thorough documentation later.