Getting Started with thesisdownrli

Source: vignettes/thesisdownrli.Rmd

It is possible to use thesisdownrli without RStudio but it will probably work best with it.

From RStudio

There are two ways to use thesisdownrli with RStudio.

  1. If you generally make use of RStudio projects then you can open a new thesis project (using thesisdownrli and bookdown) from the list of New Project options.

This will create a new RStudio project in a folder containing all the template files needed.

  1. If you don’t use RStudio projects you can create a similar template folder from an R Markdown template. Use File -> New File -> R Markdown… then choose From template, then choose Thesis-RLI, and enter index as the Name. This will create a new folder titled index. Once this has been created you can rename the folder. Note: The temporary files will currently only Knit if you name the directory index when creating it.

Without RStudio

If you’re not using RStudio, run this line in your R console to create a new PhD dissertation from the template:

Creating Your Thesis

If you have followed the steps above then hopefully you will have a new folder containing some template R markdown files amongst other things. To test whether everything is working ok you should now open the file named index.Rmd (if it isn’t already open) and click the Knit button at the top.

Alternatively, if you’re not using RStudio, you can use the line of code below, assuming your have set the index/ directory as your working directory:

bookdown::render_book('index.Rmd', thesisdownrli::thesis_pdf(latex_engine = 'xelatex'))

The PDF file of your thesis will be deposited in the _book/ directory. In most instances it will also either open automatically or prompt that RStudio blocked a pop-up.

Components

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

_bookdown.yml

This is the main configuration file for your thesis. It determines what Rmd files are included in the output, and in what order. Arrange the order of your chapters in this file and ensure that the names match the names in your folders. For more details please see the relevant section of the complete bookdown book.

index.Rmd

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

01-chap1.Rmd, 02-chap2.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. For more details on R markdown please see the R markdown vignette.

bib/

Store your bibliography (as bibtex files) here. You will find a template thesis.bib to get started with. We recommend using the citr addin and Zotero to efficiently manage and insert citations. For more details on referencing please see the referencing vignette.

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.