main.rmd

---
title: "Example R Markdown Report"      #
author: Ian Cornelius                   # Sets the required information to generate a title page
date: January 2021 \newpage             #
output:
    bookdown::pdf_document2:           # Sets the output of the file to PDF
        includes:
            in_header: latex_packages.tex       # A LaTeX package MUST be used to use acronyms
bibliography: main.bib
csl: apa.csl
---
```{r load-packages, include=FALSE}
library(dplyr)      # Required to use the %>% function
library(magrittr)   # Required to use the %>% function
library(kableExtra) # Required to place the tables in the document in their correct location
```
[comment1]: <> (Creates the list of tables for any tables used)
\newpage
\listoftables

[comment2]: <> (% Creates the list of figures for any figures used)
\newpage
\listoffigures

[comment3]: <> (Creates the glossary list)
\newpage
\printnoidxglossaries

[comment4]: <> (Sample structure for a dissertation)
\newpage
# Introduction
`r lorem::ipsum(paragraphs = 2)`

[comment5]: <> ('lorem::ipsum' is being used to provide some default filler text)

[comment6]: <> (Example of using a sub-section within a section)
## Aims and Objectives
`r lorem::ipsum(paragraphs = 2)`

[comment7]: <> (Example of using a sub-sub-section within a sub-section)
### Motivation
`r lorem::ipsum(paragraphs = 2)`

\newpage
# Literature Review
`r lorem::ipsum(paragraphs = 2)`

\newpage
# Methodology
`r lorem::ipsum(paragraphs = 2)`

\newpage
# Implementation
`r lorem::ipsum(paragraphs = 2)`

\newpage
# Evaluation
`r lorem::ipsum(paragraphs = 2)`

\newpage
# Conclusion
`r lorem::ipsum(paragraphs = 2)`

[comment8]: <> (Example on how to use tables)
\newpage
# Table Example
Tables work a little differently in R Markdown, and I would always recommend using a CSV file to import your data. It make it easier when it comes to referencing the table.
The first table of this document is shown in Table \@ref(tab:table1).
```{r table1, echo=FALSE}
data <- read.csv("example_data.csv")
knitr::kable(data, caption = "The first table in this document.") %>%
        kable_styling(latex_options = "hold_position") %>% row_spec(0,bold=TRUE)
```
[comment9]: <> (Example on how to use figures)
\newpage
# Figure Example
The first figure of this document is shown in Figure \@ref(fig:image1).

```{r image1, fig.align = 'center', out.width = "60%", fig.cap = "This is the first image in this document.", echo=FALSE}
knitr::include_graphics(here::here("placeholder_image.jpg"))
```
Whilst the second figure of this document is shown in Figure \@ref(fig:image2).
```{r image2, fig.align = 'center', out.width = "60%", fig.cap = "This is the second image in this document.", echo=FALSE}
knitr::include_graphics(here::here("placeholder_image.jpg"))
```

[comment10]: <> (Example on how to use acronyms. This is very similar to how it is done in LaTeX, in fact, it is LaTeX code. R Markdown does not have a function for this.)
\newpage
# Acronyms Example
At the beginning of this document I have defined some acronyms/initialisms. For example, when I want to refer to \gls{ai} it will first say the meaning and then provide the initials in brackets. Then whenever I mention \gls{ai} at a later point, it will always be referred to by its initialism.

[comment11]: <> (Example on how to use references)
\newpage
# Reference Example
Here I am introducing you all to the wonderful work that I did as a PhD student; that is
sarcasm [@Cornelius2017Dynamic]. But as @Cornelius2017Dynamic discuss in their work, it is pretty awesome; you should **check** \underline{it} *out*.

\newpage
# Bibliography