## Activate the Core Packages
library(readr) ## Read square data; make a tibble
library(tidyverse)
library(gt) ## Tables
## Specialized Packages
library(lubridate) ## Date functions6 Bibliographic Citations
Most scientific reports need a proper bibliography.
There are a lot of difficulties in building and using bibliographic entries. The goal here is to provide a straight forward solution that works in the context of R.
You’ll use tools outside of R to collect and format bibliographic citations. Most of the focus here is on the storage of the citations and their use in various reports.
6.1 Basic Concepts
Bibliographic citations are kept in a file. Each entry is in the BibTex format. The order of the citations is not important. There may be more citations in this file than will be used in a document.
The BibTex format for a simple citation looks like the following.
@article{monson2008,
title={Cognitive-behavioral conjoint therapy for post-traumatic stress disorder: Application to operation enduring and Iraqi freedom veterans},
author={Monson, Candice M and Fredman, Steffany J and Adair, Kathryn C},
journal={Journal of Clinical Psychology},
volume={64},
pages={958–971},
year={2008},
url={https://doi.org/10.1002/jclp.20511},
doi={10.1002/jclp.20511}
}Each citation has a unique “key” that is used for reference. In the example above, the key is monson2008. This key is used in the text of a report to link to the full citation. The formats for using keys is shown later in the examples.
The full bibliography, which is usually added to the end of a report, is automatically built. Each time a new key is used as a reference in the report, the corresponding citation is added to the set of citations that will form the full bibliography. The bibliography is automatically formatted in a specific style so that there is uniformity in the presentation.
The mechanics of this system require specifications in the YAML at the start of the R document. These include the name of the file holding the citations and the desired output formatting. An example of the YAML additions is shown below.
output: html_document
bibliography: references.bib
csl: biomed-central.csl6.2 The Bib File
Creating (and maintaining) a bibliographic citation file is the first focus. There are many ways to get citations. The follow examples show some labor-saving techniques.
6.2.1 Get citations from scientific papers
Reading the scientific literature is the most common way to get citations. Many citations have a DOI number. You can use this link in RStudio’s DOI support (see below) to add the citation to your bibliography. If there isn’t a DOI link, you can copy the citation and paste it into a ChapGPT request (see below).
6.2.2 Find & format a citation with Google Scholar
Searching is Google Scholar might be helpful if you have incomplete citation information for a reference. When you find the citation, click the “cite” button and you’ll get a reference in several styles. You can get the citation in BibTeX format (note the button at the bottom).
6.2.3 Use RStudio’s Insert DOI to add a citation
First, find a DOI reference for a citation you want to use and copy it. Then, using RStudio, go to the Insert menu and select Citation … (also CTRL + Shift + F8). From the My Sources list, choose From DOI and paste the DOI reference into the box. Click the Insert button. This does two things: it adds the citation to your bibliography and it enters the citation reference to the text at the location of your cursor.
If this is the first reference in your bibliography, RStudio creates a file references.bib to hold this and future citations.
You can look at this bibliography file, edit it, and make manual additions, by opening it in RStudio (just like the Quarto files you’ve been creating).
6.2.4 Reformat a reference using ChatGPT
ChatGPT seems to be pretty good at manipulating “traditional” literature citations so they are in the BibTex format.
Copy the citation text. In ChatGPT, enter the following prompt and then paste the citation text onto the end of the prompt.
Make a BibTex format entry for the following bibliographic citation.ChatGPT will do the reformatting and provide the BibTex formatted result in a box with a copy button. Click the button and you can then past the citation into your references.bib file.
6.3 Using Citation References
Insert a literature reference by typing the bibliographic entry’s key into the text. There are two formats that you’ll likely use.
Reference in parentheses. Use square bracket, then put the key after an “@” sign. Separate multiple reference keys with semicolons.
Name in the text, date in parentheses. Type the name in the text, followed by the key after an “-@” sign within square brackets.
Here are some examples.
Conjoint therapy [@monson2008] is critical. is displayed as Conjoint therapy (Monson, Fredman, and Adair 2008) is critical.
Literate programming [@knuth1984; @ramsey1994] is now popular. is displayed as Literate programming (Knuth 1984; Ramsey 1994) is now popular.
Name in the text, date in parentheses. Type the key in the text. Note that a multi-author citation is handled with “et al.” for the authors beyond the third one.
Specialists, such as @monson2008, advocate conjoint therapy. is displayed as Specialists, such as Monson, Fredman, and Adair (2008), advocate conjoint therapy.
In this context, @Iannone2023 show a better approach. is displayed as In this context, Iannone et al. (2023) show a better approach.
References
Iannone, Richard, Joe Cheng, Barret Schloerke, Ellis Hughes, Alexandra Lauer, and JooYoung Seo. 2023. Gt: Easily Create Presentation-Ready Display Tables.
Knuth, D. E. 1984. “Literate Programming.” The Computer Journal 27 (2): 97–111. https://doi.org/10.1093/comjnl/27.2.97.
Monson, Candice M., Steffany J. Fredman, and Kathryn C. Adair. 2008. “Cognitivebehavioral Conjoint Therapy for Posttraumatic Stress Disorder: Application to Operation Enduring and Iraqi Freedom Veterans.” Journal of Clinical Psychology 64 (8): 958–71. https://doi.org/10.1002/jclp.20511.
Ramsey, Norman. 1994. “Literate Programming Simplified.” IEEE Software 11 (5): 97–105.