A Template for creating a PhD Thesis at American University using R Markdown based on the AU LaTeX thesis template and the R Bookdown package
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README.md

eagledown

This GitHub repository provides an R Markdown template for writing a PhD Thesis at American University based on the AU LaTeX thesis template and the R Bookdown package. The AU LaTex template itself uses the AU thesis class. The template has been modified to be readable in R Markdown. Other than setting the respective folder paths for the required .clo files, the thesis class has not been modified.

This project was inspired by by the thesisdown, huskydown and bookdown packages. Unlike thesisdown and huskydown, which provide instructions how to work with bookdown and markdown as the substantive template content, eagledown provides the exact wording of the AU LaTeX thesis template. Rendering eagledown thus replicates the content found in the AU LaTex thesis template. I made this choice to make the template immediately applicable to AU students' needs. If you are new to working with bookdown and rmarkdown, please read over the excellent documentation provided by thesisdown, huskydown and in the bookdown book.

The focus of this project lies heavily on the PDF version, since this is the only format that the AU administration accepts. The PDF version is fully functional. The word, gitbook and epub versions are currently mere placeholders and have no templates behind them. I might develop them at a later time if needed/wanted.

Required external installations

In order to compile PDF documents using use R, you need to have R, Pandoc, and LaTeX installed.

You can download the respective platform-dependent version of R here for Mac and here for Windows.

You can download RStudio here. RStudio comes with Pandoc already installed.

The easiest way to install LaTeX on any platform is through tinytex:

install.packages(c('tinytex', 'rmarkdown'))
tinytex::install_tinytex()
# after restarting RStudio, confirm that you have LaTeX with 
tinytex:::is_tinytex()

If you'd rather install the full-fledged version of LaTeX (my personal preference), you can download the respective platform-dependent version here. Note that the full version tends to be very large, in the realm of several GB.

Installing eagledown

The easiest way to use eagledown is within RStudio:

  1. Install the bookdown and eagledown packages (and previously devtools, dplyr, and ggplot2, since those are needed by the template content):
install.packages("devtools", repos = "http://cran.rstudio.org")
install.packages("dplyr")
install.packages("ggplot2")
devtools::install_github("rstudio/bookdown")
devtools::install_github("SimonHeuberger/eagledown")
  1. Open RStudio and select File -> New File -> R Markdown...

  2. Choose 'From template', then choose 'AU-Thesis.

  3. Browse to the folder Location of your choice and provide a Name. Name will be the name of the folder where your dissertation will be stored. Let us use the name "actual_thesis" here.

If you are not using RStudio, run this line in your R console to create a new PhD thesis from the template:

rmarkdown::draft('actual_thesis.Rmd', template = 'thesis', package = 'eagledown', create_dir = TRUE)

Components of eagledown

_book/

This folder contains the files thesis.tex and thesis.pdf (after rendering). The files names are specified in _bookdown.yml (see below). thesis.pdf is your dissertation as a PDF.

_bookdown_files/

This folder contains the folders thesis_cache and thesis_files. This is where files produced by rendering are saved.

_bookdown.yml

This file specifies the order of .Rmd files in your dissertation. It is the main configuration file for your thesis. It determines what Rmd files are included in the output, and in what order. Arrange the order of your chapters in this file and ensure that the names match the names in your folders. The current order is: .Rmd, 01-chap1.Rmd, 02-chap2.Rmd, 03-chap3.Rmd, 04-conclusion.Rmd, 98-appendix.Rmd, 99-references.Rmd (as specified by the AU LaTeX template, references come at the end, after the appendix). You can also adjust the name of the resulting dissertation PDF. It is currently set to thesis. The resulting PDF is saved in the _book folder (see above).

01-chap1.Rmd, 02-chap2.Rmd, 03-chap3.Rmd, 04-conclusion.Rmd

These are the .Rmd files for the first four chapters in your dissertation (with the first being the Introduction and the last being the Conclusion). Write your content in each respective one. You do not kneed to knit these chapters individually. Simply write your content and save the file.

98-appendix.Rmd

This file contains the content of the Appendix. Since the AU thesis class requires the Appendix to be named differently, this chapter is separate from the other .Rmd chapters. Write your Appendix content here. You do not kneed to knit these chapters individually. Simply write your content and save the file.

99-references.Rmd

This file contains the heading for the Bibliography. This chapter is unnumbered. The actual Bibliography will be filled in automatically when rendering (see below). You do not need to write any content in this file.

actual_thesis.Rmd

This file knits all .Rmd files together into one PDF. It contains all the meta information that goes at the beginning of your dissertation, such as your name, degree, and your dissertation chair. This is also where you write the content of the Abstract and the Acknowledgements (if you want to include those), and where you set the location of the .csl and .bib files. This file also loads the R packages required to render eagledown.

bib/

This folder stores the bibliograhpy file (here references.bib).

figures/

This folder contains the figures loaded by the .Rmd files (here pic1.png, i.e. the AU logo)

sources/

This folder contains the template files apa.csl, auecon.clo, aut12.clo, authesis.cls, and template.tex. The first three have not been modified. The last has been modified to work in R Markdown.

Rendering your dissertation

Open _bookdown.yml and change index.Rmd to the folder name you have given in step (4) in the eagledown installation above. If you have named the folder "actual_thesis", then change index.Rmd to actual_thesis.Rmd.

Open actual_thesis.Rmd in RStudio and then click the "Knit" button. This will produce thesis.pdf, which will be saved in the book/ folder.

If you're not using RStudio, you can use the following from the R console, assuming your have set the actual_thesis/ directory as your working directory:

bookdown::render_book('actual_thesis.Rmd', eagledown::thesis_pdf(latex_engine = 'xelatex'))

Day-to-day writing of your dissertation

You need to edit the individual chapter .Rmd files to write your thesis. You also need to provide your Bibliography .bib file in the /bib folder. If you need any additional LaTex packages that are not currently loaded, simply add them to template.tex using the command usepackage{}. Other than that, you do not need to edit any other files.

Changes/Adjustments made to the AU LaTeX thesis template

I made several changes/adjustment to the AU LaTeX thesis template in order to improve the display and to fully utilize the power of R Markdown.

(1) Chapter 1: I added an R code chunk that creates a table using the R package stargazer. stargazer in R Markdown allows you to directly produce tables in the resulting PDF without actually having to modify the LaTeX table code. It is all done within the stargazer commands. The created table follows the same layout specifications as all other tables.

(2) Chapter 2: I added a few sentences to show how to link to an equation and to explain why it is currently not possible to do math equations with $$ markdown commands to produce an AU dissertation. I also added one sentence to explain why it is better to use the LaTeX itemize environment instead of markdown lists for your dissertation.

(3) Chapter 3: I deleted empty figure place-holders (First figure in second section, Second figure in second section, First figure in third section, Second figure in third section) because they appeared jumbled up. The AU thesis class specifies all figures to appear at the top of the page. Without any accompnaying text, the placement of these empty figures simply looks weird. I also added a markdown-produced figure and how to link to it. One of the most powerful aspects of R Markdown is the ability to produce figures directly from R, without having to save and load figure files into LaTeX. The added markdown-produced figure follows the same layout specifications as all other figures. I also added a few sentences to explain the differences in linking between a file-loaded figure and a markdown-produced figure.

(4) Finally, I included non-colored document links (to footnotes, to referred chapters/figures/tables) because they are very useful for committee members to review your dissertation. I also fixed two typos in the AU LaTeX thesis template in section 3.4.

Personal preferences

If you are writing in RStudio, I find the wordcount addin very useful for getting word counts and readability statistics in R markdown documents. I also recommend using the citr addin to insert citations.

If you are working on a Mac, I highly recommend using BibDesk to create and manage your bibliography.

Finally, if you are using stargazer to create tables, I highly recommend this cheat sheet.

Related projects

This project has drawn directly on code and ideas from the following:

Contributing

If you would like to contribute to this project, please start by reading the Guide to Contributing. Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.