Writing your dissertation with aggiedown

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# Writing your dissertation with <code>aggiedown</code>
### Ryan Peek
### 2019/02/12

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# What is `aggiedown`?

An Rmarkdown template which allows you to write your dissertation using RMarkdown files.

<br>

- Helpful if you are doing a bulk of your work in R/RStudio

- Eliminates hassle of trying to format your dissertation over and over again

- click `Knit` and render a UC Davis approved pdf file you can show to all your friends and family<sup>1</sup>

<br>
<center><i>
*insert cool hex design here*
</i></center>

.footnote[
[1] Or maybe your committee.
]

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# Getting Started

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### Update R and RStudio

- Seems simple, but many issues come from trying to work with different (older) versions. 
- For this demo, I'm using `R 3.5.2 (2018-12-20)`
- and RStudio `Version 1.1.463`

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### Visit the `aggiedown` [README](https://github.com/ryanpeek/aggiedown)

Walk through the installation code...the trickiest bits are typically associated with making sure you have a working LaTeX/MiKTex/MacTeX/TinyTeX version. More on this later.

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### Don't *froget* to name your document `index`

![:scale 50%](https://github.com/ryanpeek/aggiedown/blob/master/ucd_dissertation_rmd.png?raw=true)

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## General Thoughts

- The idea is to allow you to focus on writing...remember the writing part

- Overall, this was really an amazing tool to get a dissertation done

- Very flexible/powerful, but remember, it's not a polished tool/package, still rough around the edges

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## Tips, Tricks, & Other Stuff

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### A few packages that came in handy:

- [`kableExtra`](https://cran.r-project.org/web/packages/kableExtra/vignettes/awesome_table_in_pdf.pdf)

- `knitr::include_graphics()` ( [see Zev Ross' blog for great rundown](https://www.zevross.com/blog/2017/06/19/tips-and-tricks-for-working-with-images-and-figures-in-r-markdown-documents/), and Yihui's `bookdown` [web-book](https://bookdown.org/yihui/bookdown/figures.html))

- [`citr`](https://github.com/crsh/citr) RStudio add-in (+Zotero) for citations.

- [cowplot](https://cran.r-project.org/web/packages/cowplot/vignettes/introduction.html) & [patchwork](https://github.com/thomasp85/patchwork) for plotting/visualization

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### Figures: Custom Caption example

- Put the caption in the regular Markdown text section, and use it as a reference in the R code chunk:

*in markdown text*

> (ref:Ch1MyFigure) Relationship between eating chocolate and feeling happy 
as is described with curvilinear regression. A) Mean happiness vs. chocolate 
eaten; B) Relative influence of type of chocolate on mean happiness.

*then the R code chunk*

````markdown
```{r MyFigure, results="asis", warnings=FALSE, messages=FALSE, fig.cap='(ref:Ch1MyFigure)', out.height='60%', echo=F}

include_graphics("figure/ch1/MyFigure_chocolateAB.pdf")
```
````

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<div class="figure">
<img src="chocolate_consumption_figureAB.png" alt="&lt;i&gt;Relationship between eating chocolate and feeling happy as is described with curvilinear regression. A) Mean happiness vs. chocolate eaten; B) Relative influence of type of chocolate on mean happiness.&lt;/i&gt;" width="2391" height="40%" />
<p class="caption"><i>Relationship between eating chocolate and feeling happy as is described with curvilinear regression. A) Mean happiness vs. chocolate eaten; B) Relative influence of type of chocolate on mean happiness.</i></p>
</div>

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## Acknowledgements

Slides created via the R package [**xaringan**](https://github.com/yihui/xaringan).

`bookdown`, `huskydown`, and `gauchodown` all crucial to getting this whole thing going.