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.

Ha!  I was trying to reduce the number of pushes I was making.  The other
issue was that in changing the variable names to get consistency between
functions I was making a set of changes that would break the package unless
they were all put up at once, so I was trying to minimize that.
Unfortunately I haven't had enough time to focus on that alone.  I'll push
now so we can see where we're at.

On Thu, Sep 25, 2014 at 8:13 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)
>
> Thanks for the update @SimonGoring <https://github.com/SimonGoring>. It
> would really help minimise issues if you didn't run your master branch out
> so far ahead of the ropensci upstream. Also, try to compartmentalise your
> commits to separate branches for separate fixes; when you merge you are
> going to pull in a lot of changes in one go, across the code base. At the
> moment this means either no-one can work on the package until you merge or
> people work on package and then have to battle merge conflicts.
>
> —
> Reply to this email directly or view it on GitHub
> <https://github.com/ropensci/neotoma/pull/142/files#r18069972>.
>