title	output
citr: RStudio Addin to Insert Markdown Citations	github_document

[](https://cran.r-project.org/package=citr) [](https://cran.r-project.org/package=citr) [](http://www.repostatus.org/#active) [](https://travis-ci.org/crsh/citr) `citr` provides functions and an [RStudio addin](https://rstudio.github.io/rstudioaddins/) 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, ~~~r install.packages("citr") ~~~ or the current development snapshot from this GitHub repository: ~~~r 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](https://rstudio.github.io/rstudioaddins/#keyboard-shorcuts) 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](http://yihui.name/knitr/demo/child/) in another R Markdown document. The expected names of a parent document default to `c("index.Rmd", "master.Rmd")`, it thus works with [`bookdown`](https://bookdown.org/) 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. ~~~r 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](https://github.com/retorquere/zotero-better-bibtex/wiki). 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. ~~~r 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](https://github.com/daattali/addinslist#readme). There you can find other useful addins, such as [rcrossref](https://github.com/ropensci/rcrossref) or [wordcountaddin](https://github.com/benmarwick/wordcountaddin). # Package dependencies ```{r dependency_plot, echo = FALSE, fig.width = 7, fig.height = 5, message = FALSE, warning = FALSE, fig.path = "tools/images/"} source("https://gist.githubusercontent.com/crsh/c906e93c260488e7363ea606243057c2/raw/f6f0fce38bc274446d205854ea35cfa03b9b1f7a/plot_dependencies.R") plot_dependencies() ```