thesisdown Murdoch University - honours thesis

This template is a modified version of thesisdowndmq from Thomas Fung's GitHub. The thesisdownmq template is inspired by the packages thesisdown and bookdown.

This template is particularly modified for usage as honours thesis (currently working on a PhD template). Please see Murdoch University documentation for specifics on thesis guidelines.

Under the hood, the Reed College LaTeX template.

To compile PDF documents using R, you are going to need to have LaTeX installed. It can be downloaded for Windows at http://http://miktex.org/download and for Mac at http://tug.org/mactex/mactex-download.html. Follow the instructions to install the necessary packages after downloading the (somewhat large) installer files. You may need to install a few extra LaTeX packages on your first attempt to knit as well.

To view an example output of the PDF document see here

Using thesisdowndmu (hons) from Siobhon Egan's GitHub

1) Install the latest RStudio

I cover detailed instruction on installing R and RStudio here

2) Install packages

Execute the following from the R console in RStudio.

Install RMarkdown package

install.packages("rmarkdown")

You'll also need the bookdown and thesisdown

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

3) Download or clone this repo

The easiest way to access and use this template is to download or clone this repo.

This can be done by going to https://github.com/siobhon-egan/thesisdownMU-honours.git and selecting the green Code button, and select Download zip.

Unzip the folder and open the thesisdownMU.Rproj.

Alternatively in the 'terminal window' within RStudio type the following

git clone https://github.com/siobhon-egan/thesisdownMU-honours.git

4) Edit the .Rmd files

Start by opening the index.Rmd file and add in all the formalities (e.g. name, supervisor, degree etc).

Note: do not change the name of the index.Rmd file.

You can remove any sections that are relavent by simply commenting them out with a #.

Files

• Files ending in .Rmd are the ones you edit. Start with the index.Rmd file and work your way through the different chapters, for example 01-chap1.Rmd for Literature review, 02-chap2.Rmd for Materials and Methods section etc.
• reedthesis.cls contains the structure and components that make up the thesis
• template.tex contains the LaTeX template of the thesis document
• _bookdown.yml outlines what files will be compiled into the final thesis document

Directories

• _book/ this is where the output documents will be stored.
• figure/ contains any images/figures that you wish to include.
• bib/ contains the bibliography file in a .bib format. I use zotero (which is free!) and integrates really well with Rmarkdown, a good explaination available here
• csl/ this is a place to store the referencing template that you wish to use, offical repository for Citation Style Language (CSL) citation styles here
• data/ folder to store any data you wish to use if run analysis or read data into your thesis document.

5) Knit to PDF

By default the document knits to PDF format.

If you want to knit the file to a different format (e.g. word or html), simply edit the output: section in the index.Rmd file. However a word of caution is this template has been optimised for PDF output and you may find formatting issues when knitting to other formats. I am trying to work on optimising this.

Default...knit to PDF

output:
  thesisdownmq::thesis_pdf: default
#  thesisdown::thesis_gitbook: default
#  thesisdown::thesis_word: default
#  thesisdown::thesis_epub: default

Change knit to html format gitbook document

output:
#  thesisdownmq::thesis_pdf: default
  thesisdown::thesis_gitbook: default
#  thesisdown::thesis_word: default
#  thesisdown::thesis_epub: default

6) Repeat!

Get writing and edit the individual chapter R Markdown files as you wish and then re-run step (5) again.

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Links to some good resources here:

• oxforddown
• Rmarkdown workshop
• R Markdown the definitive guide
• R for data science