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.

Yes, sorry.  I'm going to try to finish this tonight.  Can you hold off on
fixes right now @gavinsimpson and @karthik?  I can take care of most of the
merge fixes I think, but I've been chasing bugs and it's going a bit slower
than I expected.
On Sep 25, 2014 7:42 PM, "Gavin Simpson" <notifications@github.com> wrote:

> In R/compile_taxa.R:
>
> > @@ -120,7 +120,7 @@ compile_taxa <- function(object, list.name, alt.table = NULL, cf = TRUE, type =
> >      }
> >
> >      if ('download' %in% class(object[[1]])) {
> > -      output <- llply(object, aggregate.counts)
> > +      output <- plyr::llply(object, aggregate.counts)
>
> This is OK for now. @SimonGoring <https://github.com/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.
>
> —
> Reply to this email directly or view it on GitHub
> <https://github.com/ropensci/neotoma/pull/142/files#r18069193>.
>