A paged html thesis template for R Markdown users

A {pagedown} template.


by


William Brent Thorne, BSc


Department of Templates


Submitted in partial fulfillment of
the requirements for the degree of


Master of Documentation


Faculty of Reproducibility and FOSS, Typeset University
St. Catharines, ON


© 2019 William Brent Thorne

This thesis entitled

A paged html thesis template for R Markdown users


by


William Brent Thorne, BSc


Submitted in partial fulfillment of
the requirements for the degree of


Master of Documentation


And has been duly approved by



Chair of Department, Dr. Jane Doe III
Faculty Advisor, Dr. John Smith
Date

Dedication

A dedication line or two goes here.

Abstract

This is the abstract.

Preface

A preface to the thesis.

Acknowledgement

Put the ackknowledgements here.

Contents

List of Tables

List of Figures

Literature Review

This is where you can include a lit review if you don’t wish for it to be an individual chapter or to be numbered. To make sure that a section heading is not numbered use the {-} notation beside the header text like this:

rmarkdown:

# Literature Review {-}

This is where you can include a lit review if you don't wish for it to be an individual chapter or to be numbered. To make sure that a section heading is not numbered use the `{-}` notation beside the header text like this:

1 The Basics

1.1 Introduction

This template is based on the pagedown::html_paged template and modified to meet the requirements of a generic thesis document. Standard RMarkdown formatting can be used for smooth and distraction free writting, for example I will add a citation for the {knitr} package which is located in the Thesis.bib file auto-generated in this template (Xie 2024).

Thanks to the help of Romain Lesur this template has the ability to tag section headers with the word “Chapter”. To have your chapters display as this one (Chapter 1 The Basics) use the {.chapter} class like this:

rmarkdown

---
output:
  pagedown::thesis_paged
    number_Sections: yes
---
# The Basics {.chapter}

## Introduction

This template is based on the `pagedown::html_paged` template...

1.2 Second level heading

Here is some code and a plot, with a figure caption, Figure 1.1:

The automatic numbering of this figure will only work if it includes a figure caption, user beware!

Figure 1.1: The automatic numbering of this figure will only work if it includes a figure caption, user beware!

Here is an example of an abbreviation where I use the <abbr> html tag BT. In the future there may be a pandoc solution to abbreviation management, however HTML is the way to go for now.

2 Understanding the method to the madness

Need formulas? Here’s some mathjax notation:

\[ \beta = \sum^{1 - k}\frac{\delta D}{\sum\frac{\Delta \gamma A}{X-i}} \]

2.1 Adding Tables

You can easily add tables to this document like so, and you can also reference them like a figure, Table 2.1:

Table 2.1: A caption for the table.
Sepal L Sepal W Petal L Petal W Species
5.1 3.5 1.4 0.2 setosa
4.9 3.0 1.4 0.2 setosa
4.7 3.2 1.3 0.2 setosa
4.6 3.1 1.5 0.2 setosa

3 The final chapter to my pretend thesis

There are still a few features that would be nice to implement in the future for this template. For instance:

  1. It would be great to have the ability to use the {redoc} package to help those who have the ever dreaded “USE WORD ONLY” supervisors.

  2. It would also be great to have the ability to generate a Reference section for each Chapter for those who are writing in the “integrated article” format.

  3. Along with that, it would be great to pull the YAML data from a child .Rmd file and use it as a way to add the Chapter titles and any other subsequent information (for example a thesis chapter can often actually be a full manuscript and or published paper which would need to have all authors listed for that chapter specifically as well as the journal publication information/ citation data).

References

Xie, Yihui. 2024. Knitr: A General-Purpose Package for Dynamic Report Generation in r. https://yihui.org/knitr/.

APPENDIX I

Sepal.Length Sepal.Width Petal.Length Petal.Width Species
5.1 3.5 1.4 0.2 setosa
4.9 3.0 1.4 0.2 setosa
4.7 3.2 1.3 0.2 setosa
4.6 3.1 1.5 0.2 setosa
5.0 3.6 1.4 0.2 setosa
5.4 3.9 1.7 0.4 setosa
4.6 3.4 1.4 0.3 setosa
5.0 3.4 1.5 0.2 setosa
4.4 2.9 1.4 0.2 setosa
4.9 3.1 1.5 0.1 setosa