Doc fixes

[gavinsimpson]

A lot of documentation fixes:

• mainly to remove \tabular macros in @return sections and or redundant \itemize{} or \describe{} environments.
• add links to functions in neotoma where these were just marked up as \code{fun_name}
• edited the function names from the old plurals to the new singular names
• removed trailing whitespace
• add some Rd macro where markdown backticks had been used

Essentially this is to try to get the manual PDF to build. This is the first tranche of changes. More coming in the next set of commits.

[SimonGoring]

You're the best @gavinsimpson! We switched to \tabular for a bunch of functions because the descriptions of the values returned looked kind of crappy. There was no space in between the value returned and the description of the value.

[gavinsimpson]

Cheers Simon. I think the convention is to add the space yourself. I may have done this incorrectly in the changes I made here and in #122 but we can revisit that later once I've looked through the PDF for any remaining problems in the rendering.

[SimonGoring]

Okay. It seems like an ugly solution. I liked the table format where the items and descriptions were nicely vertically aligned.

On Fri, Aug 22, 2014 at 11:53 AM, Gavin Simpson notifications@github.com wrote:

Cheers Simon. I think the convention is to add the space yourself. I may have done this incorrectly in the changes I made here and in #122 https://github.com/ropensci/neotoma/pull/122 but we can revisit that later once I've looked through the PDF for any remaining problems in the rendering.

— Reply to this email directly or view it on GitHub https://github.com/ropensci/neotoma/pull/121#issuecomment-53088619.

[gavinsimpson]

Okay. It seems like an ugly solution. I liked the table format where the items and descriptions were nicely vertically aligned.

They are only non-aligned where you've used used long component names :-) The intention is that these lists should look like the Argument lists.

There isn't an awful lot we can do about this; the \value{} section is documented to be a \describe{} environment in LaTeX and hence you can only include \item{}{} elements in this environment, plus prepended text in the form of sentences or paragraphs.

[SimonGoring]

Maybe I'll shorten components. Point made :)