To specify multiple *.bib files, one might use one of the two specifications below in the YAML.

bibliography:
- BrotherBear.bib
- ReproducibleResearch.bib
- SmokingExample.bib
- PackagesUsed.bib

OR

bibliography: ["BrotherBear.bib", "ReproducibleResearch.bib", "SmokingExample.bib", "PackagesUsed.bib"]

A cls file is used to format the citations in the text and the bibliography. Here are a few examples you can specify under the YAML csl: option:

Citing while writing

My little brother has been busy making tools (Arnholt and Mair 2002) and helping people (Abadie, Arnholt, and Miller 2010; Lopez and Arnholt 2007).

Reproducible research is critical to science (Peng, Dominici, and Zeger 2006; Fomel and Claerbout 2009; LeVeqije, Mitchell, and Stodden 2012; Peng 2011; Hutton and Henderson 2015).

Automagic Generation of R Package References

Suppose the following R packages are used for a project: PASWR2, PDS, ggplot2, knitr, and rmarkdown.

  1. Create an object named PackagesUsed.
  2. Write the packages used to a *.bib file.
  3. Load the packages with lapply().
PackagesUsed <- c("PASWR2", "PDS", "ggplot2", "knitr", "rmarkdown")
# Write bib information
knitr::write_bib(PackagesUsed, file = "PackagesUsed.bib")
# Load packages
lapply(PackagesUsed, library, character.only = TRUE)

This document uses (not really) ggplot2 by Wickham et al. (2018), PDS by A. Arnholt (2016), PASWR2 by A. T. Arnholt (2016), rmarkdown by Allaire et al. (2018), and knitr by Xie (2018).

References

Abadie, Wesley M., Jonathan L. Arnholt, and Lee A. Miller. 2010. “Dysgenesis of the Middle Turbinate: A Unique Cause of Nasal Airway Obstruction.” Otolaryngology – Head and Neck Surgery 143 (2): 317–18. doi:10.1016/j.otohns.2010.02.020.

Allaire, JJ, Yihui Xie, Jonathan McPherson, Javier Luraschi, Kevin Ushey, Aron Atkins, Hadley Wickham, Joe Cheng, Winston Chang, and Richard Iannone. 2018. Rmarkdown: Dynamic Documents for R. https://CRAN.R-project.org/package=rmarkdown.

Arnholt, Alan. 2016. PDS: Data Sets for Passion Driven Statistics. https://github.com/alanarnholt/PDS.

Arnholt, Alan T. 2016. PASWR2: Probability and Statistics with R, Second Edition. https://CRAN.R-project.org/package=PASWR2.

Arnholt, Jonathan L., and Eric A. Mair. 2002. “A ‘Third Hand’ for Endoscopic Skull Base Surgery.” The Laryngoscope 112 (12): 2244–9. doi:10.1097/00005537-200212000-00021.

Caraballo, Ralph S., Scott P. Novak, and Katherine Asman. 2009. “Linking Quantity and Frequency Profiles of Cigarette Smoking to the Presence of Nicotine Dependence Symptoms Among Adolescent Smokers: Findings from the 2004 National Youth Tobacco Survey.” Nicotine & Tobacco Research, January, ntn008. doi:10.1093/ntr/ntn008.

Chen, Kevin, Denise B Kandel, and Mark Davies. 1997. “Relationships Between Frequency and Quantity of Marijuana Use and Last Year Proxy Dependence Among Adolescents and Adults in the United States.” Drug and Alcohol Dependence 46 (1–2): 53–67. doi:10.1016/S0376-8716(97)00047-1.

Dierker, Lisa C., Eric Donny, Stephen Tiffany, Suzanne M. Colby, Nicholas Perrine, and Richard R. Clayton. 2007. “The Association Between Cigarette Smoking and DSM-IV Nicotine Dependence Among First Year College Students.” Drug and Alcohol Dependence 86 (2–3): 106–14. doi:10.1016/j.drugalcdep.2006.05.025.

Dierker, Lisa, Jianping He, Amanda Kalaydjian, Joel Swendsen, Louisa Degenhardt, Meyer Glantz, Kevin Conway, et al. 2008. “The Importance of Timing of Transitions for Risk of Regular Smoking and Nicotine Dependence.” Annals of Behavioral Medicine: A Publication of the Society of Behavioral Medicine 36 (1): 87–92. doi:10.1007/s12160-008-9051-x.

Fomel, Sergey, and Jon F. Claerbout. 2009. “Reproducible Research.” Computing in Science & Engineering 11 (1): 5–7. doi:10.1109/MCSE.2009.14.

Hu, Mei-Chen, Bengt Muthén, Christine Schaffran, Pamela C. Griesler, and Denise B. Kandel. 2008. “Developmental Trajectories of Criteria of Nicotine Dependence in Adolescence.” Drug and Alcohol Dependence 98 (1–2): 94–104. doi:10.1016/j.drugalcdep.2008.04.017.

Hutton, L., and T. Henderson. 2015. “Towards Reproducibility in Online Social Network Research.” IEEE Transactions on Emerging Topics in Computing PP (99): 1–1. doi:10.1109/TETC.2015.2458574.

LeVeqije, R.J., I.M. Mitchell, and V. Stodden. 2012. “Reproducible Research for Scientific Computing: Tools and Strategies for Changing the Culture.” Computing in Science Engineering 14 (4): 13–17. doi:10.1109/MCSE.2012.38.

Lopez, Manuel A., and Jonathan L. Arnholt. 2007. “Safety of Definitive in-Theater Repair of Facial Fractures.” Archives of Facial Plastic Surgery 9 (6): 400–405. doi:10.1001/archfaci.9.6.400.

Peng, Roger D. 2011. “Reproducible Research in Computational Science.” Science (New York, N.y.) 334 (6060): 1226–7. doi:10.1126/science.1213847.

Peng, Roger D., Francesca Dominici, and Scott L. Zeger. 2006. “Reproducible Epidemiologic Research.” American Journal of Epidemiology 163 (9): 783–89. doi:10.1093/aje/kwj093.

Riggs, Nathaniel R., Chih-Ping Chou, Chaoyang Li, and Mary Ann Pentz. 2007. “Adolescent to Emerging Adulthood Smoking Trajectories: When Do Smoking Trajectories Diverge, and Do They Predict Early Adulthood Nicotine Dependence?” Nicotine & Tobacco Research: Official Journal of the Society for Research on Nicotine and Tobacco 9 (11): 1147–54. doi:10.1080/14622200701648359.

Rose, Jennifer S., Lisa C. Dierker, and Eric Donny. 2010. “Nicotine Dependence Symptoms Among Recent Onset Adolescent Smokers.” Drug and Alcohol Dependence 106 (2-3): 126. doi:10.1016/j.drugalcdep.2009.08.012.

Van De Ven, M. O. M., P. A. Greenwood, R. C. M. E. Engels, C. A. Olsson, and G. C. Patton. 2010. “Patterns of Adolescent Smoking and Later Nicotine Dependence in Young Adults: A 10-Year Prospective Study.” Public Health 124 (2): 65–70. doi:10.1016/j.puhe.2009.11.009.

Wickham, Hadley, Winston Chang, Lionel Henry, Thomas Lin Pedersen, Kohske Takahashi, Claus Wilke, and Kara Woo. 2018. Ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics. https://CRAN.R-project.org/package=ggplot2.

Xie, Yihui. 2018. Knitr: A General-Purpose Package for Dynamic Report Generation in R. https://CRAN.R-project.org/package=knitr.