library(RefManageR)
bib <- ReadBib(system.file("Bib", "biblatexExamples.bib", 
                           package = "RefManageR"), check = FALSE)
BibOptions(check.entries = FALSE, style = "markdown", bib.style = "alphabetic", cite.style = 'alphabetic')

This is an R Markdown document. This is an example of a citation in the text Herrmann, Öfele, Schneider et al. [Her+06]. Now we cite in parentheses [e.g., BL04]. You can change the default options in a setup chunk at the start of the document or at any other point using the BibOptions function or by specifying options as a list in the .opts argument to the cite functions.

These are reports Chiu and Chow [CC78]; Padhye, Firoiu, and Towsley [PFT99]. Their hyperlinks go to their entry in the bibliography. The link for [Mar05] will take you to the document in a new window; this is the default behaviour, if a link is available (see ?open.BibEntry). The following citation has no hyperlink [Gee85]. You can also embed plots, for example:

plot(cars)

I've added a reference to CTAN without citing it. Look at all my Aristotle: [Ari07; Ari29; Ari68; Ari77].

plot(cars)

Some papers on the arXiv are Baez and Lauda [BL04]; Baez and Lauda [BL04]; Itzhaki [Itz96]; Wassenberg and Sanders [WS10].

References

[Ari07] Aristotle. De Anima. Ed. by R. D. Hicks. Cambridge: Cambridge University Press, 1907.

[Ari29] Aristotle. Physics. Trans. by P. H. Wicksteed and F. M. Cornford. New York: G. P. Putnam, 1929.

[Ari68] Aristotle. Poetics. Ed. by D. W. Lucas. Clarendon Aristotle. Oxford: Clarendon Press, 1968.

[Ari77] Aristotle. The Rhetoric of Aristotle with a commentary by the late Edward Meredith Cope. Ed. by E. M. Cope. With a comment. by E. M. Cope. Vol. 3. 3 vols. Cambridge University Press, 1877.

[BL04] J. C. Baez and A. D. Lauda. “Higher-Dimensional Algebra V: 2-Groups”. Version 3. In: Theory and Applications of Categories 12 (2004), pp. 423-491. arXiv: math/0307200v3.

[BL04] J. C. Baez and A. D. Lauda. Higher-Dimensional Algebra V: 2-Groups. Oct. 27, 2004. arXiv: math/0307200v3.

[CC78] W. W. Chiu and W. M. Chow. A Hybrid Hierarchical Model of a Multiple Virtual Storage (MVS) Operating System. Research rep. RC-6947. IBM, 1978.

[CTAN06] CTAN. The Comprehensive TeX Archive Network. 2006. URL: https://www.ctan.org (visited on 10/01/2006).

[Gee85] I. de Geer. “Earl, Saint, Bishop, Skald~- and Music. The Orkney Earldom of the Twelfth Century. A Musicological Study”. PhD thesis. Uppsala: Uppsala Universitet, 1985.

[Her+06] W. A. Herrmann, K. Öfele, S. K. Schneider, et al. “A carbocyclic carbene as an efficient catalyst ligand for C-C coupling reactions”. In: Angew.~Chem. Int.~Ed. 45.23 (2006), pp. 3859-3862.

[Itz96] N. Itzhaki. Some remarks on 't Hooft's S-matrix for black holes. Mar. 11, 1996. arXiv: hep-th/9603067.

[Mar05] N. Markey. Tame the BeaST. The B to X of BibTeX. Oct. 16, 2005. URL: http://tug.ctan.org/tex-archive/info/bibtex/tamethebeast/ttb_en.pdf (visited on 10/01/2006).

[PFT99] J. Padhye, V. Firoiu, and D. Towsley. A Stochastic Model of TCP Reno Congestion Avoidance and Control. Tech. rep. 99-02. Amherst, Mass.: University of Massachusetts, 1999.

[WS10] J. Wassenberg and P. Sanders. Faster Radix Sort via Virtual Memory and Write-Combining. Aug. 17, 2010. arXiv: 1008.2849v1 [cs.DS].