gjkerns / penguindown

An updated R Markdown YSU thesis template using the bookdown package

penguindown

This project was inspired by the thesisdown package and is an updated version of the Thesis template in thesisdown package, modified to meet YSU Graduate College standards here. It was originally designed to be a standalone LaTeX document, then was later updated to work with Sweave, and has now been translated to thesisdown. See here for many examples of theses at other institutions.

Currently, the PDF version is fully-functional. The word version is developmental, has no template behind it, and is essentially a call to the appropriate functions in bookdown.

If you are new to working with bookdown/rmarkdown, please read over the documentation available in the gitbook template at https://ismayc.github.io/thesisdown_book.

The current output is here:

• PDF (Generating LaTeX file is available here with other files in the book directory.)

Under the hood, the YSU LaTeX template is used to ensure that documents conform precisely to submission standards. At the same time, composition and formatting can be done using lightweight markdown syntax, and R code and its output can be seamlessly included using rmarkdown.

Using penguindown from gjkerns’ GitHub

Using {penguindown} has some prerequisites which are described below. To compile PDF documents using R, you are going to need to have LaTeX installed. By far the easiest way to install LaTeX on any platform is with the tinytex R package:

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

You may need to install a few extra LaTeX packages on your first attempt to knit as well. Here is one such example of how to do so:

tinytex::tlmgr_install("babel-portuges")

To use {penguindown} from RStudio:

1. Ensure that you have already installed LaTeX and the fonts described above, and are using the latest version of RStudio. You can use penguindown without RStudio, but RStudio is probably the easiest tool for writing both R code and text in your thesis. It also provides a nice way to build your thesis while editing. We’ll proceed assuming that you have decided to use the RStudio workflow.

2. Install the {bookdown}, {thesisdown}, and {penguindown} packages. Note that {thesisdown} and {penguindown} are not available on CRAN at the moment and that’s why install.packages("thesisdown") won’t work. Use remotes::install_github() as shown below instead to install the package.

   if (!require("remotes")) 
     install.packages("remotes", repos = "https://cran.rstudio.org")
   remotes::install_github("rstudio/bookdown")
   remotes::install_github("ismayc/thesisdown")
   remotes::install_github("gjkerns/penguindown")

          Note that you may need to restart RStudio at this point for the following dialog to show up.

3. Get started with the {penguindown} template. Create a new RStudio project with a {penguindown} template.

In RStudio, click on File > New Project > New Directory. Then select Thesis Project (YSU) using penguindown from the dropdown that will look something like the image below. You’ll see the graduation cap as the icon on the left for the appropriate project type. Don’t select the {thesisdown} version unless you are a student at Reed College.

Next, give your project a name and specify where you’d like the files to appear. In the screenshot below, the project name is my_thesis and it will appear as a new folder on my Desktop.

4. After choosing which type of output you’d like in the YAML at the top of index.Rmd, Knit the index.Rmd file to get the book in PDF format.

Day-to-day writing of your thesis

You need to edit the individual section R Markdown files to write your thesis. It’s recommended that you version control your thesis using GitHub if possible. RStudio can also easily sync up with GitHub to make the process easier. While writing, you should git commit your work frequently, after every major activity on your thesis. For example, every few paragraphs or section of text, and after major step of analysis development. You should git push at the end of each work session before you leave your computer or change tasks. For a gentle, novice-friendly guide to getting starting with using Git with R and RStudio, see https://happygitwithr.com/.

Rendering

To render your thesis into a PDF, open index.Rmd in RStudio and then click the “knit” button. To change the output formats, look at the output: field in index.Rmd and comment-out the formats you don’t want.

The PDF file of your thesis will be deposited in the _book/ directory, by default.

Components

The following components are ones you should edit to customize your thesis:

_bookdown.yml

This is the main configuration file for your thesis. You can change the name of your outputted file here for your thesis and other options about your thesis here.

index.Rmd

This file contains all the meta information that goes at the beginning of your document. You’ll need to edit the top portion of this file (the YAML) to put your name on the first page, the title of your thesis, etc.

01-section.Rmd, 02-section.Rmd, etc.

These are the Rmd files for each section in your thesis. Write your thesis in these. If you’re writing in RStudio, you may find the wordcount addin useful for getting word counts and readability statistics in R Markdown documents.

bib/

Store your bibliography (as bibtex files) here. We recommend using the citr addin and Zotero to efficiently manage and insert citations.

csl/

Specific style files for bibliographies should be stored here. A good source for citation styles is https://github.com/citation-style-language/styles#readme.

figure/ and data/

Store your figures and data here and reference them in your R Markdown files. See the bookdown book for details on cross-referencing items using R Markdown.