Tips for using RStudio or Markdown to produce your dissertation
If you are using RStudio or Markdown, here are some tips that might help make your report look great.
Don’t post process in Word
When you are in the final stages of producing your document, you may find it desirable to (a) include a flashy front page (b) append additional pdfs. Avoid the temptation to use Microsoft Word to do this as it reformats the content dramatically.
Instead, you can use
---
...
header-includes:
- \usepackage{pdfpages}
---
...
```{=latex}
\includepdf[pages=-]{added.pdf}
```
What about a flashy front page?
Keep your title page simple—it really only needs to have the title and author. All the information about who the supervisor is and so forth can be put underneath the declaration. You don’t even need your student number since all documents are submitted online and indelibly associated with your id already.
If you really want a fancy front page and are using the scrbook document class, you can do something like:
---
title: false
documentclass: scrbook
...
---
```{=latex}
\frontmatter
\begin{titlepage}
\hfill\includegraphics[height=1.5cm]{logo}\par%
{\centering
\vspace{0.2cm}
{\usekomafont{title}\Huge My Wonderful Work\par} % <<<
{\usekomafont{subtitle} Put subtitle here\par} % <<<
\vspace{1.3cm}
\includegraphics[width=0.8\columnwidth]{yourimagehere}\par %<<<
{\usekomafont{caption}Source: where it came from\par}
{\usekomafont{author} Your name and student id here\par}
{\usekomafont{date} \today}
}
\end{titlepage}
%
```
Number sections
By default, RStudio / pandoc does not number section headings. To fix this, in the YAML header, use something like:
---
...
output:
pdf_document:
number_sections: true
---
This should automatically number your sections.
Selecting the LaTeX class
I personally prefer the KOMA report class over the LaTeX default. I usually turn off the geometry and subtitle packages as well.
--- ... documentclass: scrreprt geometry: false subtitle: false ---
Inserting LaTeX commands into your text
You can insert a block of LaTeX commands directly into your text by wrapping them like so:
```{=latex}
\frontmatter
\tableofcontents
\mainmatter
```
The above example is also great when using scrreprt or scrbook to insert the table of contents and to number the first few pages with roman numerals instead of arabic numbers. If you have an appendix, you’ll also want to use \backmatter.
Including images
The documentation for referencing images is here: https://pandoc.org/MANUAL.html#images. Images need to sit in a file and they then get included into the document when it is compiled. The syntax is something like:
Note the hint about `implicit_figures’, which means that if you include alternative text (that’s the text in square brackets) and put the image in its own paragraph (which means, leave a blank line before and after), then it will be turned into a figure float.
Don’t be afraid to put lots of description in your caption as this will be helpful to the reader. Captions that just say “Results” or “Graph of performance” are not so useful. More useful captions should contain 2 or more sentences and should make the figure understandable without reference to the main text.
Citations
The first thing to know is that to cite a paper with RMarkdown, you need to use the @ citation syntax.
The thing after @ is the citation key.
Note that you either put the citation in square brackets (for parenthetical citations) or put it without brackets when you want to refer directly to something that the authors did.
For example, if we have a paper with key Krizhevsky2012, we might refer to it as, “The ImageNet classification problem has been examined using DCNNs [@Krizhevsky2012]”.
In this case, we use square brackets so that the citation is formatted with parentheses.
Alternatively, we can put the authors as actors by saying, ”@Krizhevsky2012 applied DCNNs to ImageNet”.
There’s great information on using Zotero with RStudio online. You will probably need to install the Better BibTex add-in for Zotero. I also recommend the Chrome extension for capturing papers to your Zotero library.
Don’t forget to use Better BibTex to export your bibliography to a bib file and refer to it in your document
--- ... bibliography: "zotero-export.bib" ... ---
Include the required sections from the Word template
Frontmatter
At the front of the document, you’ll need this bit from the word template:
**Declaration of Originality**
I declare that this project is all my own work and has not been copied
in part or in whole from any other source except where duly
acknowledged. As such, all use of previously published work (from books,
journals, magazines, internet etc.) has been acknowledged by citation
within the main report to an item in the References or Bibliography
lists. I also agree that an electronic copy of this project may be
stored and used for the purposes of plagiarism prevention and detection.
**Statement of copyright**
I acknowledge that the copyright of this project report, and any product
developed as part of the project, belong to Coventry University.
Support, including funding, is available to commercialise products and
services developed by staff and students. Any revenue that is generated
is split with the inventor/s of the product or service. For further
information please see
[www.coventry.ac.uk/ipr](http://www.coventry.ac.uk/ipr) or contact
<ipr@coventry.ac.uk>.
**Statement of ethical engagement**
I declare that a proposal for this project has been submitted to the
Coventry University ethics monitoring website
(https://ethics.coventry.ac.uk/) and that the application number is
listed below (Note: Projects without an ethical application number will
be rejected for marking)
[Signed:]{.underline} [Date:]{.underline}
Please complete all fields.
-----------------------------------------------------------------------
First Name:
--------------------- -------------------------------------------------
Last Name:
Student ID number
Ethics Application
Number
1^st^ Supervisor Name
2^nd^ Supervisor Name
-----------------------------------------------------------------------
**This form must be completed, scanned and included with your project
submission to Turnitin. Failure to append these declarations may result
in your project being rejected for marking.**
Other sections to include
The template suggests the following section headings. Pay attention, however to what it says in the marking scheme rather than slavishly adhere to these headings.
# Abstract
I recommend that you write a maximum of 3 sentences on each of:
1. motive
2. method
3. results
4. conclusions
# Introduction
Introduce your work by describing the motivation briefly (but do not just reproduce your abstract).
You should also give a paragraph on the aim of the work.
Finally, you can describe the structure of the document (no more than 2 or 3 sentences on this).
The whole introduction should fit on about one page.
Avoid covering background (e.g., introduction to reinforcement learning) -- leave that for the literature review.
# Literature review
This should cover everyone else's work in this area.
If you are reproducing a paper, look at what papers they reference as a guide but don't be limited by this.
## Sub area 1
It often makes sense to break down your literature review using sub headings.
## Sub area 2
Here is another sub heading.
# Methods and materials
If you have experimental equipment, here is where you describe it.
If you use specific software tools, you can describe that here.
It is also a good idea to discuss any technique used to help ensure results were rigorous (such as, cross validation).
Make sure you don't just mention the method, but also describe how it was used.
# Results
Make sure you only put your own results and work here.
Refer back to the literature section if needed.
# Project management
Describe any overall approaches used for project management, such as: Agile, Feature Driven Development, V-model, or Spiral Model.
## Project schedule
I prefer this to be a simple table but you can show a Gantt chart if you prefer.
## Risk management
Describe realistic risks (not just the bad things that actually happened).
It is not necessary to describe VDU usage hazards.
Present them in a table layout and include columns for likelihood, impact, and mitigation.
## Quality management
What did you do to check your results? For example, did you code unit tests?
Did you get a critical friend or your supervisor to review your document?
## Social, legal, ethical and professional considerations
This should focus on the project and its potential for societal impact in the future.
You need to show that you have considered these issues but you shouldn't list spurious or frivolous issues.
# Critical appraisal
If some things didn't work, this is your chance to reflect on what you learned from the process.
# Conclusions
## Achievements
## Future work
# References
(note: it should not be called "bibliography")
```{=latex}
\backmatter
\appendix
```
# Project presentation
# Certificate of ethics approval
Word count
You should aim for around 8,000 words. Although the upper limit is stated as 15,000, this is definitely more than desirable.
Including code blocks
To include properly formatted code, use three backquotes followed by the name of the language in curly braces and end the block using another three backquotes.
You will probably need eval=FALSE to stop evaluation of the code.
Here’s an example:
```{python eval=FALSE}
import numpy as np
print("hello world")
```
The first time you try this, you may find it needs a package called reticulate.
This can be installed from the Tools menu.