• Advanced topics in markup languages and literate programming.

  • R Markdown Headers

  • Footnotes

  • BibTeX/Pandoc and citing R Packages

  • Time consuming analyses: caching and Make files

Proposal for your Collaborative Research Project.

Deadline: 28 October

Submbit: A (max) 2,000 word proposal created with R Markdown. The proposal will:

• State your research question. And justify why it is interesting.

• Provide a basic literature review (properly cited with BibTeX).

• Identify data sources and appropriate research methodologies for answering your question.

As always, submit the entire GitHub repo.

Definitely see me with your ideas/draft.

Start thinking about types of statistical models that you want to use.

An example of a paper + analysis + data project using many of the tools we cover today is available at:

HertieDataScience/Examples/SimplePaperWithAnalysis

An R Markdown file is just a text file with markup instructions that RStudio understands.

The key to document-consistent formatting is the header.

It is at the start of a file and comes between ---.

The header is written in YAML.

YAML is a human read-able data format.

Elements are separated from values with a colon (:).

Each element is separated by new lines.

Hierarchy is maintained with tabs.

---
title: 'MPP-E1180 Lecture 5'
author: "Christopher Gandrud"
date: "22 February 2016"
output:
  ioslides_presentation:
    css: css/font-awesome.min.css
    logo: img/logo.png
  beamer_presentation: default
---

YAML is a recursive acronym: ''YAML Ain't Markup Language''.

By defualt, R Markdown uses the ioslides HTML presentation slides style.

You can also use reveal.js.

First install the revealjs R package:

devtools::install_github("jjallaire/revealjs")

Then in the YAML header use:

output: revealjs::revealjs_presentation

For further styling see https://github.com/jjallaire/revealjs

You can add a table of contents and numbered sections to your PDF output:

output:
  pdf_document:
    toc: true
    number_sections: true
    fig_captions: true

To do the same for HTML also include the information under html_document.

Create consistent figure formatting:

output:
  pdf_document:
    fig_width: 7
    fig_height: 6
    fig_caption: true

fig_caption: true attaches captions to figures.

To set the actual caption label, use the fig.cap='SOME CAPTION' code chunk option.

R Markdown can use Pandoc footnotes.

In-text: In the text place a unique footnote key in the format:

• [^KEY]

At the end of your document put the full footnote starting with the key, e.g.

• [^KEY]: This is a footnote.

BibTex allows you to create a database of all of the literature/packages you cite.

You can then insert them into your text and they will:

• Be automatically formatted consistently.

• Generate an appropriately ordered, consistently formatted reference list at the end of your document with only the works you actually cited.

A BibTeX database is just a text file with the extension .bib.

Each entry follows a standard format depending on the type of media.

@DOCUMENT_TYPE{CITE_KEY,
    title = {TITLE},
    author = {AUTHOR},
    . . . = {. . .},
}

Note: Commas are very important!

The cite key links a specific citation in your presentation document to a specific BibTeX database entry.

They must be unique.

It does not matter what order your BibTeX entries are in the .bib file.

@article{Acemoglu2000,
    author = {Acemoglu, Daron and Robinson, James A.},
    title = {Why Did the West Extend the Franchise? Democracy, Inequality,
            and Growth in Historical Perspective},
    journal = {The Quarterly Journal of Economics},
    year = {2000},
    volume = {115},
    number = {4},
    pages = {1167--1199},
}

@book{Cox1997,
    title={Making Votes Count: Strategic Coordination in the World's
            Electoral Systems},
    author={Gary W. Cox},
    year={1997},
    volume = {7},
    publisher={Cambridge University Press},
    address = {Cambridge}
}

For more media types and entry fields see http://en.wikipedia.org/wiki/BibTeX.

Google scholar generates BibTeX entries.

On an entry click Cite > BibTeX.

For a YouTube how-to see https://www.youtube.com/watch?v=SsJSR2b4_qc.

Sometimes they need to be cleaned a little.

To link your .bib file to your RMarkdown document add to the header:

bibliography:
    - BIB_FILE_NAME.bib
    - ANOTHER_BIB_FILE_NAME.bib

Note: The files should be in the same directory as your R Markdown file.

R Markdown uses Pandoc syntax to include a citation in-text.

General format: @CITE_KEY.

So if the cite key is Box1973 then @Box1973 will return Box and Tiao (1973) in the text of the presentation document.

A reference list with the full bibliographic details of all cited documents will be automatically created at the end of your document.

Tip: Put # References at the very end of your R Markdown document to have a section heading before the reference list.

Why cite?

• Give credit to the software authors (just like when citing literature).

• Enable reproducible research: identify which software you used and which version.

Base R way: print citation, copy BibTeX entry into your .bib file.

Cite R:

toBibtex(citation())

## @Manual{,
##   title = {R: A Language and Environment for Statistical Computing},
##   author = {{R Core Team}},
##   organization = {R Foundation for Statistical Computing},
##   address = {Vienna, Austria},
##   year = {2016},
##   url = {https://www.R-project.org/},
## }

Cite R Packages:

toBibtex(citation('dplyr'))

## @Manual{,
##   title = {dplyr: A Grammar of Data Manipulation},
##   author = {Hadley Wickham and Romain Francois},
##   year = {2016},
##   note = {R package version 0.5.0},
##   url = {https://CRAN.R-project.org/package=dplyr},
## }

The dynamic literate programming way: Use LoadandCite from the repmis package.

Load all of the packages at the beginning of you R Markdown file in a chunk with include=FALSE.

LoadandCite loads the packages and creates a BibTeX file with all of the citations.

pkgs <- c('dplyr', 'ggplot2')

repmis::LoadandCite(pkgs, file = 'RpackageCitations.bib')

Note: Use a file name that is different from your literature BibTeX file!

Include the .bib file in your RMarkdown header.

Each cite key follows: R-PKG_NAME.

R itself has the key CiteR.

So @R-dplyr and @CiteR create the citations:

• Wickham and Francois (2016)

• R Core Team (2016)

Knitting your analysis and presentation documents together by placing all of your R code into code chunks can sometimes be problematic:

• When they are time consuming: requires a lot of computational time.

• When they access files over the internet: bad practice to make many repeated calls to the same URL, can crash the site. This is equivalent to a denial-of-service attack.

• When they are many lines long.

• Long lines: use source() to run R code in other files.

• Caching for time/computationally intensive work: cache=TRUE code chunk option: only runs the chunk when the chunk code changes.

Make files are the ultimate solution to these problems.

Make is a command line program.

Big Idea: run a make file that runs a list of specific files in order.

Files are only run if they have been changed since the last time the make file was last run.

See Ch. 6 of RRRR if you might want to do this.

Clone the HertieDataScience/Examples repo and play around with SimplePaperWithAnalysis.

Begin working with your partner on your research proposal.

• Identify the research area and key literature.

• Create a new repo and R Markdown document for your proposal.

• Begin building a BibTeX database for your key literature and try including them in your proposal.

• Begin identifying data sources.