citr: RStudio Addin to Insert Markdown Citations

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

Installation

~~You can either use the stable version of citr from CRAN,~~ Due to an intermittently orphaned dependency, citr is currently not on CRAN. Due to continuing SARS-CoV-2 related lockdowns, I’m having trouble allocating time to a resubmission. In the meantime, please install citr from this GitHub repository (see below).

# install.packages("citr")

or the current development snapshot from this GitHub repository:

devtools::install_github("crsh/citr")

How to use citr

The RStudio addin

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 bibliography files 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 bibliography 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")).

Using citr without RStudio

The following call searches a bibliography 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.

Better BibTeX integration

If you are using Zotero citr can access your reference database
directly. For this to work, you need to install the Better BibTeX
extension.
Once the extension is installed and your reference manager is running,
citr can access all your references and keep your bibliography file
updated by adding missing references.

Tidying bibliography files

When you are done writing, your bibliography 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 bibliography file.

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

Known problems

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 BibTeX-plugin allows users to specify fields to omit:

Once, the above error has occurred, it may be necessary 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.

Other RStudio addins

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.