Pandoc Yaml Bibliography Meaning

For starters, this is how you might want to turn your well-written Markdown file (with common metadata fields like , and ) into a properly typeset PDF document:

However, Markdown is not TeX. Not even close. Once you need to have some bleeding edge control over the typesetting outcome, or perhaps just a little refinement on its LaTeX templating, you’ll soon notice that Pandoc has its quirks and gotchas. I’ve been utilizing Pandoc in all my serious academic writing (incl. homework reports) for years, ever since I gave up on learning more about the overwhelmingly sophisticated TeX ecosystem and turned to something that “just works”. Pandoc fits my needs well. And when it doesn’t, there’s almost always a workaround that achieves the same thing neatly. And this is what this write-up is mostly about.

Tweaking ? Bad idea.

You could, of course, modify the default template () provided by Pandoc, as long as you’re no stranger to LaTeX. In this way, you can achieve anything you want – in pure LaTeX.

There are, however, a few problems with this naïve approach:

  1. If you are tweaking the template just for something you’re currently working on, you will end up with some highly document-specific, hardly reusable template. Also this won’t give you any good for using Pandoc – you could just write plain LaTeX anyway.
  2. If Pandoc improves its default template for a newer version, your home-brewed template won’t benefit from this (unless you’re willing to merge the diffs and resolve any conflicts by hand).

I’m conservative about changing the templates. If it’s a general issue that needs to be fixed in the default template, sending a pull request to pandoc-templates might be a better idea. Of course, if there’s a certain submission format you have to stick with (given LaTeX templates for conference papers), then you will fall back on your own.

Separating the formatting stuff

I wouldn’t claim that I know the best practice of using Pandoc, but there’s such a common idiom that cannot be overstressed: Separate presentation and content!

In the YAML front matter of (the main Markdown file you’re writing), put only things that matter to your potential readers:

And in a separate YAML file (let’s call it ), here goes the formatting stuff:

Above is my personal default, and it’s worth a few words to explain:

  • is where you control the geometric settings of your document. For example, you may narrow down the page margin to , and this is equivalent to raw LaTeX:
  • Set to any value other than if paragraph indentation is desired. (And it is often desired in formal publications.)
  • is where you define your own macros, configure existing ones, or claim in case you want to use a package not enabled by Pandoc (e.g., ). Although you might as well define those in other places (e.g., in the content of a Markdown file), don’t do that.
    • This decent Q.E.D. tombstone: is my favorite of all time. It doesn’t require the package.

With a separate , now here we are:

Citing sources

While the Markdown syntax for citing is rather easy (), it takes effort to make things right, especially if you have a certain preferred citation format (APA, MLA, Chicago, IEEE, etc.).

The suggestion is: Use pandoc-citeproc. Once you have a list of references you’re interested in, you need two things to typeset those nicely in your document:

  • A CSL (Citation Style Language) file (), to specify the citation format you want to use.
  • A BibTeX file (), which is a list of all entries you might cite.
    • Citation entries in BibTeX format may be found easily on the Internet, through academic search engines and databases. Concatenate them one by one.

As part of the YAML metadata: (Assume you have and )

Using as a filter, generate the document with citations:

The list of references is appended to the end of the document. It is often desirable to give the references an obvious title (“References”), start from a new page and avoid any further indentation, so the following comes in the end of the Markdown source:

Putting it all together!

Basically, we need 5 files in total:

  • For content:
    • (Markdown + possibly LaTeX mixed format): Main text.
    • (BibTeX/BibLaTeX format): List of references.
  • For presentation:
    • (YAML format): Format-related metadata.
    • (LaTeX format): Content of ; package imports and macro definitions.
    • (CSL XML format): Citation style.

And one command:

Open question: Lightweight replacement for ?

Pandoc doesn’t provide native support for (and I wonder if there will ever be). You can still have the same thing in Pandoc Markdown:

However, everything in between and will be treated as raw LaTeX, and the expressiveness of Markdown is lost there. More importantly, this is purely a LaTeX-specific thing, so there’s no way for Pandoc to convert this to HTML or any other format (unless you have a filter that does the trick). Consequently, I tend to write all definitions / theorems (lemmas, claims, corollaries, propositions…) in simple Markdown:

It does have some advantages over :

  • Using , you cannot see the numbering of each theorem (definition, etc.) in the text editor (well, you can’t without a dedicated plugin at least). This is inconvenient when you need to refer to a prior one later. By numbering them explicitly, you can clearly see these ordinals in the Markdown source.
  • It is perfectly valid Markdown, so it converts to any format as you wish (HTML, for example).

This also has some drawbacks compared to using , though:

  • It doesn’t have theorem counters. You need to number things explicitly, manually. (Clearly you can’t have implicit numbering and explicit numbering at the same time, so here’s the trade-off.)
  • It doesn’t have automatic formatting. That is, you could possibly get the style for a certain entry (plain, definition, remark) wrong.
  • Semantically, they are not recognized as theorems, just normal text paragraphs. This is problematic if you want to prevent definitions and theorems from being indented, since there’s no way for LaTeX to tell them from a normal text.

(Probably) The best solution is to write a filter that (conventionally) converts any plain text like (and , , etc.) in the beginning of a paragraph to proper Markdown (for HTML target) or corresponding block (for LaTeX target). Even better, it should be able to do cross-references accordingly (Remember ? Let’s put an anchored link on that!). This is yet to be done, but would be very helpful to someone who does a lot of theorems and proofs thus wants to avoid the kludge of mixing raw LaTeX with semantically evident Markdown.

So as a grad student, I write a lot. Like, a lot a lot. And as a part of that, I cite a lot of articles and books. And there are, of course, those few articles that I find myself citing in nearly every paper I write. So ideally, I could have one central repository for all of the papers that I want to be able to cite, and reference that from whatever paper I’m working on. Then, whatever program I’m using to convert the plain text to a good looking document (LaTeX, for example) should be able to take combine the citations from the text of the document with the information from this central repository and output properly formatted citations, as well as a properly formatted bibliography. Luckily, this is very easy to do.

The big picture is that you’ll keep all of your references in a .bib file. You can call it anything, so long as the file extension is .bib. My default name for these is , but you can really use whatever. Then, LaTeX (or markdown, if you’re using that) can talk to this file using a program called BibTeX. So in your LaTeX document, all you need to do to cite something is call a simple command (, for example) and then insert a “key” linking what you want to cite with an entry in the .bib file. Then, at the end of your LaTeX document, you can simply tell it to include a bibliography and specify the style you want (APSR, for example). All of the formatting and inserting the actual citation will be taken care of. Magically, in my opinion.

So although there’s a bit of setup cost, once you’ve done that (once), you can just write your document and simply drop in citations with a simple command (like ). Good editors will let you search through your .bib file for the reference you want without actually opening it. The format of the citations and the reference list will be automatically inserted and properly formatted.

It will seem a little overwhelming to set up, but fear not. It is actually really simple. Setup may take a bit, but once you have that down you shouldn’t need to do it again. Even if you do (say, for a second computer), it will be much easier.

The .bib file

In my last post, I briefly mentioned that you should write your files in plain text. This applies to your bibliography files as well. There is a pretty standardized way to format your bibliography files: the “.bib” file. Your .bib file contains information about each reference you want. So, for example, if you wanted to cite Understanding Interaction Models (which everyone should read), your .bib file would contain something like the following:

The says to begin a new reference. We then say what kind of thing it is (in this case, an article). Everything between the curly braces is information about the reference. So we have information about the title, author, the journal that it’s in, etc. The very first thing (“brambor2006” in this case) is called a bibtex key. That’s how you’ll link up the references in your LaTeX (or markdown or whatever) file to the references in your .bib file. Lucky for us, we don’t actually have to remember how to format all this. Do google scholar search, and underneath the reference that we want, click “cite” then click “BibTeX” in the window that pops up. It should then pop up with information similar to what I’ve posted above. I very rarely actually ever look at the bib file directly, since there are tons of great programs out there that will generate it for you.

Let me be clear - this .bib file is all you need to do reference management from a LaTeX document. Everything else I suggest here are simply tools to make it easier to manage your .bib file or to integrate it into your writing.

Using the .bib file in LaTeX

There are two different programs and two different packages in LaTeX to manage your bibliography. This answer to a stackexchange question gives a really good idea of the difference between them. The main gist is that biblatex (and biber) are more current programs, whereas natbib (and bibtex) are slightly older. I’d recommend using biblatex (and biber) if you’re just starting, as they offer a lot of advantages over natbib and bibtex. For the reasons you might prefer one over the other, look at the stackexchange answer linked above. You’ll probably be fine using either combination.

Basically, biblatex and natbib are LaTeX packages that enable all the citation commands that you want. Biber and BibTeX are the backends that do the hard work of linking up your .tex and .bib files to properly format all the citations and the reference list. The differences between the two in practice are minimal.

BibLaTeX and Biber

BibLaTeX and biber are the newer, snazzier versions of natbib and BibTeX. As such, they come with plenty of support for things that natbib and BibTeX either can’t do (or don’t do well).

To use them, you’ll need to enable biblatex in your preamble. Somewhere, you can add . The options are actually a bit important here. For example, you can set the citation style. The most common one that I use is . I also like to set the backend (which is probably just an old habit - biblatex used to set the backend as BibTeX instead of biber). So I usually do That produces citations in the author-year format, like (Lastname 1999), which is the most common in political science. There are other citation styles that you can check out with a quick Google search, if you need them.

The second part is to tell biblatex/biber where your .bib file is. You do this with the command. Inside the curly braces should be the path to your .bib file, relative to where your .tex file is. So if you put your .bib file in the same folder as your .tex file, all you need to do is specify the name of your .bib file. For example, if you’ve named it “library.bib”, then you simply need to place it in the same folder and then put . You can specify relative or absolute file paths if you want.

At the end of your document (but before , you’ll want to add a command command). This will actually put in a reference list at the end.

Now you’re all good to go! You can cite things with the usual biblatex reference commands. will create a citation to the bibtexkey. Autocite will attempt to create the best kind of citation from available information (like citestyle, etc). You can specify citation styles more fully with commands like , which specifies that the citation should be in parentheses. is similar, except it creates a citation as a footnote. There are other commands you can use, which are all easily found online.

Natbib and BibTeX

Natbib and BibTeX are the older cousins of BibLaTeX and biber. They are very similar in use. You need to tell LaTeX that you’re using natbib using the command. You set up the bibliography using the command (you can put in ) there for APSR-type citations. At the end of the document, put to use your .bib file. Like biblatex, natbib supports relative and absolute file path names.

Once you’ve done all that, you can actually start citing things in your document. In natbib, there are two main ways to cite things: and . will enclose the citation in parentheses while will print out a citation with the author’s name in text and the year in parentheses.

Using .bib in ®markdown

Since rmarkdown really wasn’t written with academic papers in mind, citations are a bit trickier. You need to specify your .bib file in the YAML frontmatter (the stuff at the top). So if your .bib file is named and is in the same folder as the .Rmd document, you can set up citations like so:

To set up the reference section, you need to put at the end of the document (remember, the symbol denotes section headings in rmarkdown). You must use pandoc-style citations. So if I wanted to reference the article from the beginning of this post, I would need to have brackets around it . That would insert a parenthetical citation. There are more examples of citation formats on rmarkdown’s website.

To tell rmarkdown (and pandoc) what citation style you want, you’ll need a .csl file. There is a large repository of these available on github and on Zotero’s website. You specify the .csl file in the YAML frontmatter in the field.

.bib file management programs

There are a lot of different programs out there that can manage your .bib file (and sync it across computers). Some of them that I know of are jabref, Mendeley, and Zotero. A few Mac people I know use Bibdesk. There’s also a program that runs in emacs that manages .bib datases (ebib). I use ebib, which I recommend if you use emacs.

For those of you who don’t use emacs, I heartily recommend Zotero. It can manage your pdf files as well as sync your bibliography across multiple computers. There is a plug in that allows you to export your bibliography as a .bib file: Better BibTeX. The Better BibTeX plugin can also keep the .bib file updated, so if you add a reference to zotero, it will automatically add it to your .bib file.

Zotero also has other features. It seems to be able to manage pdf files and images and whatnot. If you aren’t writing in plain text, Zotero can also integrate with Word and OpenOffice.

Auto-completion

This is just a quick note about auto-completion. You need to get an editor that has auto-completion for your references. It will make your life so much easier. So, for example, one way to cite things in LaTeX is with the command. A good editor will connect your .bib file and your .tex file intelligently so that you don’t have to remember all those bibtex keys. So, for example, you can just type and it will pop up with a list of completions. The best programs will let you search your .bib file and find the reference you want. The best of the best (e.g. emacs) let you search via title, author(s), year, etc.

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