Doc fix

I fixed a bunch of documentation issues. You'll need to update your roxygen too. 
There are several placeholders for @params that you'll need to flesh out before shipping to CRAN
I updated my bio in the README and also turned functions into fixed width code.

This is OK for now. @SimonGoring may already have gone through and removed this - his branch is way ahead with several commits so I suspect merge issues when he wants to merge with this upstream if we pull this in. I'm going to remove all these plyr calls at a future point anyway, once Simon merges.