A paged html thesis template for R Markdown users

In pagedown: Paginate the HTML Output of R Markdown with CSS for Print

knitr::opts_chunk$set(echo = FALSE,
                      fig.align = 'center')

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:

The Basics {.chapter}

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 [@R-knitr].

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...

Second level heading

Here is some code and a plot, with a figure caption, Figure \@ref(fig:code):

plot(iris$Sepal.Length,
     iris$Sepal.Width,
     col = iris$Species,
     pch = 19)

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.

Understanding the method to the madness {.chapter}

Need formulas? Here's some mathjax notation:

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

Adding Tables

You can easily add tables to this document like so, and you can also reference them like a figure, Table \@ref(tab:atable):

knitr::kable(
  iris[1:4, 1:5],
  align = 'c',
  caption = 'A caption for the table.',
  col.names = c("Sepal L", "Sepal W", "Petal L", "Petal W", "Species")
)

The final chapter to my pretend thesis {.chapter}

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 {-}

knitr::write_bib(c('knitr', 'rmarkdown', 'xaringan'), 'packages.bib')

APPENDIX I {-}

knitr::kable(iris[1:10,1:5], align = 'c')

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