In cjvanlissa/worcs: Workflow for Open Reproducible Code in Science

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
library(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 citekeys 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. Seaching 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.

knitr::include_graphics("scholar_bib.png")

cjvanlissa/worcs documentation built on Nov. 7, 2024, 1:20 p.m.