biblioformat: Revise and Reformat Plain Text Bibliographies with R

This package aims to help with revising and reformatting reference lists (bibliographies) in plain text format. It takes a reference list as plain text, tries to retrieve DOIs and metadata from Crossref, and reformat them according to a chosen style (e.g. BibTeX, or following a particular journal citation style).

Installation

devtools::install_github("Pakillo/biblioformat")

Motivation

The motivation for this package is the need to revise and/or reformat reference lists (bibliographies) only available as plain text (e.g. at the end of a manuscript or document). This happens e.g. when our manuscript is rejected from a journal and we need to reformat the bibliography and we don't have the original bibliographic database (as BibTeX, Mendeley, Zotero...) but only a plain text of references.

This package takes the text with references, tries to identify their DOIs and metadata at Crossref, and outputs the revised citations in the chosen format (BibTeX, a particular journal style...).

Example

For example, if we have these references that we want to check (and optionally reformat):

Foster, G. et al. (2017) Future climate forcing potentially without precedent in the last 420 million years.

Chen, I.-C. et al. (2011) Science 333, 1024-1026

We can copy them to the clipboard or provide them as a character vector:

refs <- c(
  "Foster, G. et al. (2017) Future climate forcing potentially without precedent in the last 420 million years.",
  "Chen, I.-C. et al. (2011) Science 333, 1024-1026"
)

then

library(biblioformat)

newrefs <- biblioformat(refs, style = "global-ecology-and-biogeography")
newrefs

#> [1] "Foster, G.L., Royer, D.L. & Lunt, D.J. (2017) Future climate forcing potentially without precedent in the last 420 million years. Nature Communications, 8, 14845."      

#> [2] "Chen, I.-C., Hill, J.K., Ohlemuller, R., Roy, D.B. & Thomas, C.D. (2011) Rapid Range Shifts of Species Associated with High Levels of Climate Warming. Science, 333, 1024–1026."

Note that missing titles and journals have now been corrected. We can use >9000 different citation styles.

The revised references are automatically copied to the clipboard, so they can be directly pasted into the original document.

Alternatively, we can obtain the references in BibTeX format, for further editing or importing into a reference manager

newrefs <- biblioformat(refs, format = "bibtex", filename = "myrefs.bib")

Note that some references may be changed and erroneously confounded with others. Please check the output reference list.

Acknowledgements

This package is just a wrapper of the excellent rcrossref package by rOpenSci - big thanks to them!

Related

See also https://anystyle.io/ for an excellent free online parser of bibliographic references. Also http://cermine.ceon.pl/cermine/index.html, and others...