Citing (aka scientific citation) is quite straight forward in RMarkdown. However, there are some shortcomings. Primarily, as citations are rendered via Pandoc’s reference engine, bibtex is used as a standard. Though is quite commonly used, bibtex has been, over and above, replaced by biblatex. biblatex is much more straight forward than bibtex (as text is formatted using latex and not bibtex, still making use of bibtex for the collection of references).

One simple way is to tell pandoc or RMkarkdown, for that matter, to use biblatex, see this post for that approach. However, there are some tweaks that allow to continue using bibtex.

For example, say you would like to show the exact date of one article; in standard bibtex it is not possible. However, the “month” field can be (ab)used for that pupose (this idea was found in this post, thanks for pointing out!).

Consider this bibtex input:

@electronic{martin_2014,
  author        = "J. Martin",
  title         = "Senator quits Montana race after charge of plagiarism",
  journal       = "New York Times",
  year          = "2014",
  month         = "Aug. 7",
  url           = "http://www.nytimes.com/2014/08/08/us/politics/john-walsh-drops-campaign-under-pressure-
from-democrats.html?_r=0",
}

It will be rendered (in APA) in this format:

Martin, J. (2014, Aug. 7). Senator quits montana race after charge of plagiarism. New York Times. Retrieved from http://www.nytimes.com/2014/08/08/us/politics/john-walsh-drops-campaign-under-pressure- from-democrats.html?_r=0

(Plus italics in the appropriate place)

@article{wang_2014,
  author        = "W. Q. Wang and H. Shao",
  title         = "High altitude platform multichannel {SAR} for wide-area and staring imaging",
  journal       = "Aerosp. and Electron. Syst.",
  volume        = "29",
  number        = "25",
  month         = "Mar 10",
  year          = "2014",
  pages         = "12--17"
}