Embedded hyperlinks in a thesis or research paper

Question

I am writing a master's thesis in engineering. It is quite literature-heavy, and I'm using Zotero with BibTeX to manage my references. For the most part, I use Zotero's browser extension to create Zotero entries, but when necessary (e.g. for PDFs that were only published on a university server), I also create some from scratch. Sometimes, I want to cite websites of software tools without a publication. I could gather as much information as possible from those websites, but since these references are really only made in passing, I find that giving the reader a URL suffices. Also, my sources list is quite long already, so I try to avoid going out of my way to add extra references just for the sake of mentioning a single name. So, a URL it is.

What is and what ought be the best practice to include such a naked URL into a master's thesis, or even a research paper? There are essentially three possible ways to do this:

1. Footnote with the link (e.g. using \url{ } from hyperref): ugly, but visible to people who print the work on physical paper -- and lose the digital version, so that the only way to visit the URL is copying it letter by letter manually. Edit: for non-homepages, I am using archive.org to prevent link rot, which is academically good, but the URLs are ridiculously unaesthetic.
2. Embedded hyperlink in the text (with an unobtrusive colour to indicate the text is clickable). Looks neat, but not accessible in print. This is what I'm currently doing.
3. Have a list of raw URLs as a subsection of my sources list, and use some LaTeX magic to annotate and jump to the correct link from the text.

Worth mentioning: our department has 1. no standard citation style and 2. stopped requiring physical thesis prints since 2020, hence why 1. I have the freedom to choose the citation style and 2. I am embracing hyperlinks currently. My thesis is in NLP, so my own style most closely resembles that of the ACL (see this paper as an example), but this is not a hard constraint.

I am asking for an ought as well because of this freedom. If the standard is (1), but there are better arguments for (2), then I prefer (2).

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Note: I am not asking how to cite a website. As explained above, I've made up my mind on this: I want to only cite a URL, not have a whole BibTeX entry for it. The question is how/where to do the citation.

Answer 1

I would put real links in an appendix, with refs that jump there in the online version but are simply text in the hard copy. That's [xxx] or [n] in the body and [\url{...}] in the appendix. That does not call for much LaTeX magic. Ask at tex SE for help if you need it.

Be sure to annotate links with a "last visited" date.

The ability to jump back to the text after viewing a reference in the appendix would be nice. That does call for a little magic.

I find footnotes distracting. Avoid them unless your discipline embraces them.

Answer 2

Ultimately, this question can only be answered by your future reader(s), which presumably will be your parents and the supervising professor (and maybe a committee), with an off-chance of others if you wrote a high impact thesis. I would not worry about your parents, but I would worry about your supervisor and your MS committee. This will also depend on whether they like to use an electronic copy or a printed one. (I prefer a printed one because it is easier to annotate.)

Citations in academic texts are about honesty (attributing other's results to them) and traceability. In the printed world, it was customary to cite editions and pages in editions so that a reader could follow up on the citation. This way, I (the reader) can look-up your (the author) resource and check whether you used it correctly, not so much to police you but to assure myself that you applied the resource correctly or represented the cited author's position correctly.

Electronic resources introduced an element of uncertainty as resources could vanish or move overnight or even be changed. The academic community dealt with this problem by using analogy. So, we used these "retrieved on a certain date" and we might now be starting to use the internet-archive to give more permanence to these resources.

Any citation-style that deals with these additional problems of electronic resources is fine in my opinion and would be judged by aesthetic criteria. But my opinion does not matter all that much to you.

Answer 3

One option you could consider is using endnotes instead of footnotes. This would avoid shortening the text on the page and diverting reader attention, while preserving the URLs for readers of printouts. It is essentially the same idea as using an appendix for the URLs, but more granular.

Answer 4

How to present links

My personal favourite technique for displaying hyperlinks is to use hyperref with options:

\hypersetup{%
colorlinks=false,% hyperlinks will be black
linkbordercolor=red,% hyperlink borders will be red
pdfborderstyle={/S/U/W 1}% border style will be underline of width 1pt
}

This produces a single coloured underline which is not visible in print. This avoids the typical ugly boxes. I recommend using different colours for links within the document and links to websites. Use a monospaced font for URLs!

Where to put links

I cannot see a compelling reason not to treat these URLs as you would any other reference. This is the simple and conventional approach. You say your reference list is already long---so a few more entries wouldn't make much difference. There are other techniques available to deal with a long reference list such as having a separate list for each section, using author-date referencing to reduce the need for the reader to visit the reference list, or otherwise splitting references into several lists.

Additionally, if you use the reference list rather than an inline URL, you would have the space to include two URLs---one being the official URL and the other being the archive.org URL. I find it odd to only provide the archive.org URL if the website is still active.