citr provides functions and an RStudio addin to search a BibTeX-file to create and insert formatted Markdown citations into the current document.

You can either use the stable version of citr from CRAN,

install.packages("citr")

or the current development snapshot from this GitHub repository:

devtools::install_github("crsh/citr")

Once citr is installed and you have restarted your R session, the addin appears in the menus. Alternatively, you can define a keyboard shortcut to call the addin.

The addin will automatically look up the Bib(La)TeX-file(s) specified in the YAML front matter. If the document does not contain a YAML front matter the addin will attempt to locate a parent document and look up the Bib(La)TeX-file specified therein. That is, the addin works its automagic even if you edit R Markdown documents that are included as children in another R Markdown document. The expected names of a parent document default to c("index.Rmd", "master.Rmd"), it thus works with bookdown out of the box, but can be customized (e.g., options(citr.parent_documents = "my_parent.Rmd")).

The following call searches a Bib(La)TeX-file and creates formatted Markdown citations for the results.

library("citr")
md_cite("foo 2016", bib_file = "references.bib")

md_cite() searches the author, year, title, and journal fields of your references.

If you are using Zotero or Juris-M citr can access your reference database directly. For this to work, you need to install the Better Bib(La)TeX extension, which I would recommend anyway. Once the extension is installed and your reference manager is running, citr will automatically access all your references and keep your Bib(La)Tex-file updated by adding missing references. If you dislike this behavior, you can disable it by setting options(citr.use_betterbiblatex = FALSE).

When you are done writing, your Bib(La)Tex file is likely to contain some unneeded references, which you added while writing but removed during revisions. tidy_bib_file() removes unneeded (or duplicate) entries from your Bib(La)Tex-file.

tidy_bib_file(
  rmd_file = "report.Rmd"
  , messy_bibliography = "references.bib"
  , file = "tidy_references.bib"
)

citr relies on RefManager::ReadBib() and, thus, indirectly on bibtex::read.bib() to load bibliographies. I have noticed that very long Bib(La)Tex fields can cause these underlying functions to fail (e.g., Error in do_read_bib(file, encoding = .Encoding, srcfile): lex fatal error: input buffer overflow, can't enlarge buffer because scanner uses REJECT). To avoid such problems, I strongly recommend to disable the export of potentially long metadata fields, such as abstract and notes. The Better Bib(La)TeX-plugin allows users to specify fields to omit:

Once, the above error has occured, it may be neccessary to restart the R session. Otherwise reading any other file may fail with Error: lex fatal error: fatal flex scanner internal error--end of buffer missed.

If you are interested in other handy addins take a look at this list. There you can find other useful addins, such as rcrossref or wordcountaddin.