# Citing references in worcs

Comprehensive citation of literature, data, materials, methods, and software is one of the hallmarks of open science. When using the R-implementation of WORCS, you will most likely be writing your manuscript in `RMarkdown` format. This means that you will use Markdown `citekey`s to refer to references, and these references will be stored in a separate text file known as a `.bib` file.

To ease this process, we recommend following this procedure for citation:

1. During writing, maintain a plain-text `.bib` file with the BibTeX references for all citations.
   - You can export a `.bib` file from most reference manager programs; the free, open-source reference manager Zotero is excellent and user-friendly, and highly interoperable with other commercial reference managers. Searching for “How to Integrate Zotero Citations with R Markdown” will yield tutorials for using Zotero with RMarkdown.
   - Alternatively, it is possible to make this file by hand, copy and pasting each new reference below the previous one; e.g., Figure @ref(fig:scholarbib) shows how to obtain a BibTeX reference from Google Scholar; simply copy-paste each reference into the `.bib` file
2. To cite a reference, use the `citekey` - the first word in the BibTeX entry for that reference. Insert it in the RMarkdown file like so: `@yourcitekey2020`. For a parenthesized reference, use `[@citekeyone2020; @citekeytwo2020]`. For more options, see the RMarkdown cookbook.
3. To indicate a non-essential citation, mark it with a double at-symbol: `@@nonessential2020`.
4. When Knitting the document, adapt the `knit` command in the YAML header.
   `knit: worcs::cite_all` renders all citations, and
   `knit: worcs::cite_essential` removes all non-essential citations.
5. Optional: To be extremely thorough, you could make a “branch” of the GitHub repository for the print version of the manuscript. Only in this branch, you use the function `knit: worcs::cite_essential`. The procedure is documented in this tutorial.

Exporting a BibTex reference from Google Scholar