The Manuscript

At the top of the file named manuscript-example.Rmd you see a YAML (Yet Another Mark Up Language) header. This header tells knitr and pandoc what exactly you want done with the document.

---
title: "A Very Serious Analysis of the Stationarity of Corn and Soybean Prices"
author: "Peter Economist, Paul Economist, Mary Economist"
date: 'May 05, 2016'
output: 
  pdf_document:
    template: simple.latex
    fig_caption: yes
documentclass: ajae
bibliography: bibliography.bib
---

Title and author are self explanatory.

date: field tells knitr to place the current date formatted in the %B %d, %Y style.

output: After knitr evaluates code chunks contained in the body of the file. The output feild tells pandoc what kind of file to create. Here we have specified to produce PDF output. PDF output is produced by pandoc creating a .tex file and if no further fields are specified there is a latex template that pandoc uses to make the docuement (based on the article class). Here we have specified to create the manuscript according to the specifications of the American Journal of Agricultural Economics (AJAE). Since they have their own latex class (ajae) that comes in the standard latex distribution we can just specify documentclass: ajae and the formatting is handled. We needed to also specify template: simple.latex because something in the pandoc template was clashing with the ajae.csl file. I removed the problem lines and saved that as simple.latex, which you can see in the root directory of this repository. We will cover how to specify different output formats in a later section.

bibliography: The file bibliography.bib is located in the root directory of this repository and it is a Bibtex database of all the references needed for the manuscript. Open this file and note what the reference entries look like. To build a database for your own paper, Google Scholar has a ‘cite’ button below every search result it returns. Click ‘cite’, then click ‘Bibtex’ and a plain text window will open with the properly formatted Bibtex entry. Just copy and paste this into bibliography.bib. The bibliography.bib file used for this tutorial is shown below.

@article{akerlof1970vthe,
title={The Market for Lemons: Qualitative Uncertainty and the Market MechanismV},
author={Akerlof, George},
journal={Quarterly Journal of Economics},
volume={84},
year={1970}
}

@article{johansen1988statistical,
title={Statistical analysis of cointegration vectors},
author={Johansen, S{\o}ren},
journal={Journal of economic dynamics and control},
volume={12},
number={2},
pages={231--254},
year={1988},
publisher={Elsevier}
}

@article{said1984testing,
title={Testing for unit roots in autoregressive-moving average models of unknown order},
author={Said, Said E and Dickey, David A},
journal={Biometrika},
volume={71},
number={3},
pages={599--607},
year={1984},
publisher={Biometrika Trust}
}

@book{enders1995applied,
title={Applied Econometric Time Series },
author={Enders, Walter},
year={1995},
publisher={Applied Economic Time Series}
}

@book{gandrud2013reproducible,
title={Reproducible Research with R and R Studio},
author={Gandrud, Christopher},
year={2013},
publisher={CRC Press}
}