huphydown

The huphydown package is an adaptation of the popular thesisdown package for writing a thesis at the Physics Institute of Humboldt-University of Berlin. The template follows that guidelines of the institute here and can be adjusted as needed in the 'template.tex' file.

This project was inspired by the bookdown package and is an updated version of my Senior Thesis template in the reedtemplates package here. It was originally designed to only work with the Reed College LaTeX template, but has since been adapted to work with many different institutions by many different individuals. Check out the Customizing thesisdown to your institution section below for examples.

Currently, the PDF and gitbook versions are fully-functional. The word and epub versions are developmental, have no templates behind them, and are essentially calls 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://thesisdown.netlify.com/. This is also available below at https://ismayc.github.io/thesisdown_book.

The current output for the four versions is here:

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

Under the hood, the HU Physics LaTeX template is used to help documents conform to submission standards, feel free to adjust those to changes in standards and personal preference. Composition and formatting can be done using lightweight markdown syntax, and R code and its output can be seamlessly included using rmarkdown.

Using huphydown

Special thanks to Ben Marwick for helping to add a lot more clarity to the directions below from the README of his spin-off huskydown package.

Using huphydown 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-german")

To use huphydown 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 thesisdown without RStudio. For example, you can write the Rmd files in your favourite text editor (e.g. Atom, Notepad++). 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 and huphydown packages. Note that huphydown is not available on CRAN at the moment and that's why install.packages("huphydown") 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("napiontek/huphydown")

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

3. Use the New R Markdown dialog to select HU Physics Thesis:

Note that this will currently only Knit if you name the directory index as shown above. This guarantees that index.html is generated correctly for the Gitbook version of the thesis.

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 or HTML formats.

Day-to-day writing of your thesis

You need to edit the individual chapter 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 between PDF, gitbook and Word , 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. Note that you need to have at least one chapter start in the index.Rmd file for the build to work. For the template, this is done with # Introduction in the example from the template.

01-intro.Rmd, 02-theory.Rmd, etc.

These are the Rmd files for each chapter in your dissertation. 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.