zoteR

An R interface to Zotero via the Better BibTeX add-on. zoteR lets you insert citations, fetch bibliography data, and keep bibliography files in sync with your Zotero library — all from R, with RStudio addin support.

Prerequisites

Installation

# install.packages("pak")
pak::pkg_install("sarcastic-scientist/zoteR")

Usage

Check connection

zt_is_running()   # TRUE if Zotero + Better BibTeX are available

Insert citations

Open the Better BibTeX cite-as-you-write picker and return a formatted citation:

# Pandoc format: [@doe2020]
zt_cite(format = "pandoc", .action = zt_insert)

# LaTeX format: \cite{doe2020}
zt_cite(format = "latex", .action = zt_insert)

Fetch bibliography data

# For specific citation keys
zt_bib(c("doe2020", "smith2019"), format = "json")

# Interactively via CAYW picker
zt_bib_cayw(format = "biblatex")

# For currently selected items in Zotero
zt_bib_selected(format = "json")

Format note: "json" (CSL-JSON) is recommended for R Markdown and Quarto documents. Other formats undergo lossy conversion when pandoc processes the bibliography.

Sync bibliography files

The primary use case is keeping a bibliography file up to date as you write. Add this to your document’s YAML front matter:

bibliography: "`r zoteR::zt_write_bib('refs.json', overwrite = TRUE)`"

Every time the document knits, zt_write_bib() detects all @key citations in the file and fetches the latest data from Zotero.

To update the bibliography file without knitting:

zt_update_bib("paper.Rmd")   # reads bibliography path from YAML front matter

Detect citations

# Scan a file for pandoc-style citation keys
zt_detect_citations("paper.Rmd")

# Scan a string
zt_detect_citations_text("See [@doe2020] and @smith2019.")

Code chunks, inline R expressions, and URLs are excluded from detection to avoid false positives. To force a key to be included (e.g. cited only in a figure caption), add it to a nocite field in your YAML front matter or in an HTML comment.

Library management

zt_libraries()              # data frame of all available libraries

# Look up library ID by name (more portable than hardcoding IDs)
zt_bib(keys, library_id = zt_library_id("Group Library Name"))

Output actions

All retrieval functions accept a .action argument that controls what happens to the result:

Action Behaviour
zt_return return invisibly (default; assign to a variable)
zt_print print to console
zt_insert insert at cursor in RStudio
zt_copy copy to clipboard

RStudio addins

Three addins are included (accessible via Addins menu or keyboard shortcuts):

Addin Function
Insert Zotero Citation Opens CAYW picker; inserts citation at cursor
Insert Zotero Bibliography (Selected Items) Inserts bibliography for items selected in Zotero
Update Bibliography for Current Document Syncs bibliography file for the active .Rmd / .qmd

Citation format (Pandoc vs. LaTeX) is detected automatically from the active file’s extension.

Package options

Option Default Description
zoter.default.format "biblatex" Default bibliography format
zoter.default.bib "biblatex" Format for .bib files ("biblatex" or "bibtex")
zoter.default.library_id 1L Default Zotero library ID 
options(zoter.default.format = "json")

License

GPL (>= 3)