# Bibliographies

## Making a bibliography

Markdown-memo uses bibtex via pandoc to generate a bibliography for your document. We’ve made this even simpler by allowing the user to create a simple text file to generate the necessary bibtex .bib file using the markdown2bib script. Markdown-memo looks for any bibs/*.txt files and uses markdown2bib to combine them and create bibs/mybib.bib in bibtex format. This is later used by pandoc when creating tex $$\rightarrow$$ pdf or html.

The bibs/*.txt should be plain text with a single reference per line, with each reference in a style that loosely follows the American Psychological Association (APA), which is commonly used in humanities. Currently four types of references are supported: article, book, incollection, and misc. The journal or book titles need to be in markdown-style emphasis, meaning *Set Within Asterixis*. Also note that for works in a collection, you need to use the word “In” in the right place, like in the reference by Quine below. The rest of the syntax tries to be forgiving. If you want to add a note to appear at the end of the reference, put it at the end within [square brackets] like the work by Plato below.

For example, the mybib.txt file in this document is

ATLAS Collaboration. (2008). The ATLAS Experiment at the CERN Large Hadron Collider. *Journal of Instrumentation*, 3, 08003. https://cds.cern.ch/record/1129811
ATLAS Collaboration. (2012). Observation of a new particle in the search for the Standard Model Higgs boson with the ATLAS detector at the LHC. *Physics Letters B*, 716, 1--29. https://arxiv.org/abs/1207.7214
Feynman, R.P. (1963). *The Feynman Lectures on Physics, Volume I*. California Institute of Technology. http://www.feynmanlectures.caltech.edu/I_03.html
Feynman, R.P. (1965). The Development of the Space-Time View of Quantum Electrodynamics. Nobel Lecture, December 11, 1965. http://www.nobelprize.org/nobel_prizes/physics/laureates/1965/feynman-lecture.html
Guest, D., Collado, J., Baldi, P., Hsu, S. C., Urban, G., & Whiteson, D. (2016). Jet flavor classification in high-energy physics with deep neural networks. *Physical Review D*, 94, 112002. https://arxiv.org/abs/1607.08633
Miller, A. (2014). Realism. *Stanford Encyclopedia of Philosophy*. http://plato.stanford.edu/entries/realism/
Plato. (2000). *The Republic*. (G. Ferrari, Ed. & T. Griffith, Trans.). Cambridge University Press. [(Originally written ca. 380 BCE)]
Quine, W.V.O. (1969). Natural kinds. In *Ontological Relativity and Other Essays* (pp. 114--138). Columbia University Press.
van Fraassen, B. (1980). *The Scientific Image*. Oxford University Press.

If you do not want to use simplified txt files to generate bibtex, and you want to write your own bibtex, then simply remove any bibs/*.txt files and write a file called bibs/mybib.bib.

If you do not need a bibliography, set

dorefs: false

in meta.yaml, and then these scripts and programs are not run.

## Doing citations

Citations start with an @-sign, and can be used inline, like:

@Miller_2014_Realism argues that we should get real.

which produces:

Miller (2014) argues that we should get real.

Inside a caption, you may want to end it with the citation in parentheses like this:

Blah blah blah [@Feynman_1963_The_Feynman_Lectures_on_Physics_Volume_I]\.

which produces:

Blah blah blah (Feynman, 1963).

Typically, I find it better to leave citations1 in footnotes to keep from cluttering the main text. Let’s try citing various kinds of references. Feynman said some important things2. But everything is a footnote to Plato3. Van4 is a cool cat too. A reference with more than 4 authors should be automatically shortened with et al.5

In order for a References section to be generated per html page, you need to add a special html comment near the end of your Markdown file for that page:

<!-- REFERENCES -->

Pages without such a comment will not get an automatic References section, but the complete pdf document will automatically still have a complete References section at the end as long as

dorefs: true

is set in meta.yaml.

## References

Feynman, R. P. (1963). The Feynman Lectures on Physics, Volume I. California Institute of Technology. http://www.feynmanlectures.caltech.edu/I_03.html

———. (1965). The Development of the Space-Time View of Quantum Electrodynamics. Nobel Lecture, December 11, 1965. http://www.nobelprize.org/nobel_prizes/physics/laureates/1965/feynman-lecture.html

Guest, D. et al. (2016). Jet flavor classification in high-energy physics with deep neural networks. Physical Review D, 94, 112002. https://arxiv.org/abs/1607.08633

Miller, A. (2014). Realism. Stanford Encyclopedia of Philosophy. http://plato.stanford.edu/entries/realism/

Plato. (2000). The Republic. (T. Griffith, Trans., G. Ferrari, Ed.). Cambridge University Press. (Originally written ca. 380 BCE).

Quine, W. V. O. (1969). Natural kinds. In Ontological Relativity and Other Essays (pp. 114–138). Columbia University Press.

van Fraassen, B. (1980). The Scientific Image. Oxford University Press.

1. Quine (1969).

2. Feynman (1965).

3. Plato (2000).

4. van Fraassen (1980).

5. Guest, D. et al. (2016).