This is my full PhD thesis in R Markdown (using the bookdown package), containing a PDF and EPUB file, and a website in the ‘docs’ folder with the integral content of the book. https://git.io/PhDthesisAMR
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phd_thesis/01-introduction.Rmd

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# Introduction {#introduction}
You can label chapter and section titles using `{#label}` after them, e.g., we can reference Chapter \@ref(introduction).
Figures and tables with captions will be placed in `figure` and `table` environments, respectively.
```{r nice-fig, fig.cap='Here is a nice figure!', out.width='80%', fig.asp=.75, fig.align='center'}
par(mar = c(4, 4, .1, .1))
plot(pressure, type = 'b', pch = 19)
```
Reference a figure by its code chunk label with the `fig:` prefix, e.g., see Figure \@ref(fig:nice-fig). Similarly, you can reference tables generated from `knitr::kable()`, e.g., see Table \@ref(tab:nice-tab).
```{r nice-tab, tidy=FALSE}
knitr::kable(
head(iris, 20), caption = 'Here is a nice table!',
booktabs = TRUE
)
```