diff --git a/.idea/misc.xml b/.idea/misc.xml
new file mode 100644
index 00000000..4eb944a0
--- /dev/null
+++ b/.idea/misc.xml
@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="JavaScriptSettings">
+    <option name="languageLevel" value="ES6" />
+  </component>
+  <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.6.0 (~/anaconda3/bin/python)" project-jdk-type="Python SDK" />
+</project>
\ No newline at end of file
diff --git a/.idea/modules.xml b/.idea/modules.xml
new file mode 100644
index 00000000..2def2a7c
--- /dev/null
+++ b/.idea/modules.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/.idea/phd_thesis_markdown.iml" filepath="$PROJECT_DIR$/.idea/phd_thesis_markdown.iml" />
+    </modules>
+  </component>
+</project>
\ No newline at end of file
diff --git a/.idea/phd_thesis_markdown.iml b/.idea/phd_thesis_markdown.iml
new file mode 100644
index 00000000..7c9d48f0
--- /dev/null
+++ b/.idea/phd_thesis_markdown.iml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$" />
+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+  <component name="TestRunnerService">
+    <option name="projectConfiguration" value="pytest" />
+    <option name="PROJECT_TEST_RUNNER" value="pytest" />
+  </component>
+</module>
\ No newline at end of file
diff --git a/.idea/vcs.xml b/.idea/vcs.xml
new file mode 100644
index 00000000..94a25f7f
--- /dev/null
+++ b/.idea/vcs.xml
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="$PROJECT_DIR$" vcs="Git" />
+  </component>
+</project>
\ No newline at end of file
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 00000000..7d954a04
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,23 @@
+FROM aergus/latex
+
+RUN apt-get update --assume-yes && \
+apt-get install --assume-yes make \
+python3-dev \
+python3-pip
+RUN tlmgr init-usertree
+RUN tlmgr install truncate \
+tocloft \
+wallpaper \
+morefloats \
+sectsty \
+siunitx \
+threeparttable
+RUN tlmgr update l3packages \
+l3kernel \
+l3experimental
+RUN python3 -m pip install pandoc-fignos pandoc-eqnos pandoc-tablenos \
+pandoc-secnos pandoc-shortcaption
+
+COPY . .
+WORKDIR /data
+ENTRYPOINT ["make"]
diff --git a/Makefile b/Makefile
index f000825c..6873f3bf 100644
--- a/Makefile
+++ b/Makefile
@@ -6,6 +6,7 @@ INPUTDIR=$(BASEDIR)/source
 OUTPUTDIR=$(BASEDIR)/output
 TEMPLATEDIR=$(INPUTDIR)/templates
 STYLEDIR=$(BASEDIR)/style
+SCRATCHDIR=$(BASEDIR)/scratch
 
 BIBFILE=$(INPUTDIR)/references.bib
 
@@ -16,43 +17,48 @@ help:
 	@echo 'Usage:                                                                 '
 	@echo '   make html                        generate a web version             '
 	@echo '   make pdf                         generate a PDF file  			  '
-	@echo '   make docx	                       generate a Docx file 			  '
-	@echo '   make tex	                       generate a Latex file 			  '
-	@echo '                                                                       '
+	@echo '   make docx	                     generate a Docx file 			      '
+	@echo '   make tex	                     generate a Latex file 			      '
 	@echo ' 																	  '
+	@echo '   multiline_tables                 convert a large markdown table into a$\'
+	@echo '									                                        multi-line format' 
 	@echo ' 																	  '
+	@echo '   tables	                       convert a md table into LaTeX, to$\'
+	@echo '                                       be used sideways or with other$\'
+	@echo '      			                       advanced formatting'															
+	@echo '                                                                       '
 	@echo 'get local templates with: pandoc -D latex/html/etc	  				  '
 	@echo 'or generic ones from: https://github.com/jgm/pandoc-templates		  '
 
 pdf:
-	pandoc "$(INPUTDIR)"/*.md \
+	pandoc  \
+	--filter=pandoc-shortcaption \
+	--filter=pandoc-xnos \
+	"$(INPUTDIR)"/*.md \
 	-o "$(OUTPUTDIR)/thesis.pdf" \
 	-H "$(STYLEDIR)/preamble.tex" \
-	--template="$(STYLEDIR)/template.tex" \
 	--bibliography="$(BIBFILE)" 2>pandoc.log \
 	--csl="$(STYLEDIR)/ref_format.csl" \
-	--highlight-style pygments \
 	-V fontsize=12pt \
 	-V papersize=a4paper \
 	-V documentclass=report \
-	-N \
 	--pdf-engine=xelatex \
 	--verbose
 
 tex:
 	pandoc "$(INPUTDIR)"/*.md \
-	-o "$(OUTPUTDIR)/thesis.tex" \
-	-H "$(STYLEDIR)/preamble.tex" \
 	--bibliography="$(BIBFILE)" \
 	-V fontsize=12pt \
 	-V papersize=a4paper \
 	-V documentclass=report \
 	-N \
 	--csl="$(STYLEDIR)/ref_format.csl" \
-	--latex-engine=xelatex
 
 docx:
-	pandoc "$(INPUTDIR)"/*.md \
+	pandoc \
+	--filter=pandoc-shortcaption \
+	--filter=pandoc-xnos \
+	"$(INPUTDIR)"/*.md \
 	-o "$(OUTPUTDIR)/thesis.docx" \
 	--bibliography="$(BIBFILE)" \
 	--csl="$(STYLEDIR)/ref_format.csl" \
@@ -61,6 +67,8 @@ docx:
 html:
 	pandoc "$(INPUTDIR)"/*.md \
 	-o "$(OUTPUTDIR)/thesis.html" \
+	--filter=pandoc-shortcaption \
+	--filter=pandoc-xnos \
 	--standalone \
 	--template="$(STYLEDIR)/template.html" \
 	--bibliography="$(BIBFILE)" \
@@ -72,4 +80,13 @@ html:
 	mkdir "$(OUTPUTDIR)/source"
 	cp -r "$(INPUTDIR)/figures" "$(OUTPUTDIR)/source/figures"
 
-.PHONY: help pdf docx html tex
+multiline_tables:
+	pandoc "$(SCRATCHDIR)/tables.md" \
+	-t markdown+multiline_tables \
+	-o "$(SCRATCHDIR)/cleaned_tables.md"
+
+tables: multiline_tables
+	pandoc "$(SCRATCHDIR)/cleaned_tables.md" \
+	-o "$(SCRATCHDIR)/tables.tex"
+
+.PHONY: help pdf docx html tex multiline_tables tables
diff --git a/README.md b/README.md
index 9c789fa4..e7747621 100644
--- a/README.md
+++ b/README.md
@@ -19,6 +19,7 @@ Markdown is a super-friendly plain text format that can be easily converted to a
 - it automatically handles the table of contents, bibliography etc with Pandoc.
 - comments, drafts of text, etc can be added to the document by wrapping them in &lt;!--  --&gt;
 - it works well with Git, so keeping backups is straightforward. Just commit the changes and then push them to your repository.
+- it is able to take advantage of autocompletion capabilities for figures and citations in several text editors (VSCode, Sublime, etc.)
 - there is no lock-in. If you decide that Markdown isn't for you, then just output to Word, or whatever, and continue working in the new format.
 
 ## Are there any reasons not to use Markdown?
@@ -37,35 +38,46 @@ There are some minor annoyances:
 - Makefile => contains instructions for using Pandoc to produce the final thesis.
 - output/ => directory to hold the final version.
 - source/ => directory to hold the thesis content. Includes the references.bib file.
+- scratch/ => directory to hold tables which can be converted between different formats.
 - source/figures/ => directory to hold the figures.
 - style/ => directory to hold the style documents.
 
 ## How do I get started?
 
-1. Install the following software:
-    - A text editor, like [Sublime](https://www.sublimetext.com/), which is what you'll use write the thesis.  
-    - A LaTeX distribution (for example, [MacTeX](https://tug.org/mactex/) for Mac users).
-    - [Pandoc](http://johnmacfarlane.net/pandoc), for converting the Markdown to the output format of your choice.  You may also need to install [Pandoc cite-proc](http://pandoc.org/demo/example19/Extension-citations.html) to create the bibliography.
-    - Install @martisak's shortcaption module for Pandoc, with `pip install pandoc-shortcaption`
-    - Git, for version control.
-2. [Fork the repository](https://github.com/tompollard/phd_thesis_markdown/fork) on Github  
-3. Clone the repository onto your local computer (or [download the Zip file](https://github.com/tompollard/phd_thesis_markdown/archive/master.zip)).  
-4. Navigate to the directory that contains the Makefile and type "make pdf" (or "make html") at the command line to update the PDF (or HTML) in the output directory.  
-**In case of an error** (e.g. `make: *** [pdf] Error 43`) run the following commands:  
-    ```
-    sudo tlmgr install truncate
-    sudo tlmgr install tocloft
-    sudo tlmgr install wallpaper
-    sudo tlmgr install morefloats
-    sudo tlmgr install sectsty
-    sudo tlmgr install siunitx
-    sudo tlmgr install threeparttable
-    sudo tlmgr update l3packages
-    sudo tlmgr update l3kernel
-    sudo tlmgr update l3experimental
-    ```
-    
-5. Edit the files in the 'source' directory, then goto step 4.  
+For both of these methods, you'll need 
+
+- A text editor like [Sublime](https://www.sublimetext.com/) or [VSCode](https://code.visualstudio.com)
+- Git for version control
+
+After installing git:
+1. [Fork the repository](https://github.com/tompollard/phd_thesis_markdown/fork) on Github  
+2. Clone the repository onto your local computer (or [download the Zip file](https://github.com/tompollard/phd_thesis_markdown/archive/master.zip))
+
+### The easy way: Docker
+
+1. Install [Docker](https://www.docker.com/get-started)
+2. Navigate into your newly cloned repository, and type
+
+    ```docker build -t denrondal/md_thesis .``` 
+
+    into the terminal. This will take several minutes.
+
+3. Now you can convert the sample dissertation to pdf:
+
+    ```docker run --volume "`pwd`:/data" dendrondal/md_thesis pdf```
+
+That's it! You should see a sample pdf in the output directory. Note that `pdf` can be subsituted with any other command. To see all commands, just run ```docker run --volume "`pwd`:/data" dendrondal/md_thesis help```
+
+### The hard way: Install everything locally
+
+1. Install the following software:  
+    - A LaTeX distribution (for example, [MacTeX](https://tug.org/mactex/) for Mac users, or [TexLive](https://tug.org/texlive/) for Linux/Windows users).
+    - [Pandoc](http://johnmacfarlane.net/pandoc), for converting the Markdown to the output format of your choice.  
+    - [Python 3](https://www.python.org/downloads/) and python3-pip
+    - Pandoc plugins by running ```bash install.sh``` in the main directory. **If you are on windows, you will need to install the pandoc plugins in this file manually**. This may work on WSL, but has not been tested.
+2. Navigate to the directory that contains the Makefile and type "make pdf" (or "make html") at the command line to update the PDF (or HTML) in the output directory.
+
+**In case of an error** (e.g. `make: *** [pdf] Error 43`), consult [this article](https://dalwilliams.info/lessons-learned-from-writing-a-phd-dissertation-in-markdown.html) for possible fixes. Most importantly, make sure tlmgr is properly installed, then run ```install.sh``
 
 ## What else do I need to know?
 
diff --git a/install.sh b/install.sh
new file mode 100644
index 00000000..e9a4b39d
--- /dev/null
+++ b/install.sh
@@ -0,0 +1,15 @@
+#!/usr/bin/env bash
+
+sudo apt-get install pandoc-citeproc &&
+sudo tlmgr install truncate &&
+sudo tlmgr install tocloft &&
+sudo tlmgr install wallpaper &&
+sudo tlmgr install morefloats &&
+sudo tlmgr install sectsty &&
+sudo tlmgr install siunitx &&
+sudo tlmgr install threeparttable &&
+sudo tlmgr update l3packages &&
+sudo tlmgr update l3kernel &&
+sudo tlmgr update l3experimental &&
+pip3 install pandoc-fignos pandoc-eqnos pandoc-tablenos \
+            pandoc-secnos pandoc-shortcaption
diff --git a/output/source/figures/example_figure.pdf b/output/source/figures/example_figure.pdf
deleted file mode 100644
index dcffff1d..00000000
Binary files a/output/source/figures/example_figure.pdf and /dev/null differ
diff --git a/output/thesis.html b/output/thesis.html
index 176f805a..abe9bf39 100644
--- a/output/thesis.html
+++ b/output/thesis.html
@@ -5,9 +5,72 @@
         <meta http-equiv="Content-Style-Type" content="text/css" />
         <meta name="generator" content="pandoc" />
         <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
-                        <title></title>
+                        <title>01_title_page</title>
         <style type="text/css">code{white-space: pre;}</style>
-                                                    <style>
+                            <style type="text/css">
+            a.sourceLine { display: inline-block; line-height: 1.25; }
+            a.sourceLine { pointer-events: none; color: inherit; text-decoration: inherit; }
+            a.sourceLine:empty { height: 1.2em; }
+            .sourceCode { overflow: visible; }
+            code.sourceCode { white-space: pre; position: relative; }
+            div.sourceCode { margin: 1em 0; }
+            pre.sourceCode { margin: 0; }
+            @media screen {
+            div.sourceCode { overflow: auto; }
+            }
+            @media print {
+            code.sourceCode { white-space: pre-wrap; }
+            a.sourceLine { text-indent: -1em; padding-left: 1em; }
+            }
+            pre.numberSource a.sourceLine
+              { position: relative; left: -4em; }
+            pre.numberSource a.sourceLine::before
+              { content: attr(data-line-number);
+                position: relative; left: -1em; text-align: right; vertical-align: baseline;
+                border: none; pointer-events: all; display: inline-block;
+                -webkit-touch-callout: none; -webkit-user-select: none;
+                -khtml-user-select: none; -moz-user-select: none;
+                -ms-user-select: none; user-select: none;
+                padding: 0 4px; width: 4em;
+                color: #aaaaaa;
+              }
+            pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa;  padding-left: 4px; }
+            div.sourceCode
+              {  }
+            @media screen {
+            a.sourceLine::before { text-decoration: underline; }
+            }
+            code span.al { color: #ff0000; font-weight: bold; } /* Alert */
+            code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
+            code span.at { color: #7d9029; } /* Attribute */
+            code span.bn { color: #40a070; } /* BaseN */
+            code span.bu { } /* BuiltIn */
+            code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
+            code span.ch { color: #4070a0; } /* Char */
+            code span.cn { color: #880000; } /* Constant */
+            code span.co { color: #60a0b0; font-style: italic; } /* Comment */
+            code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */
+            code span.do { color: #ba2121; font-style: italic; } /* Documentation */
+            code span.dt { color: #902000; } /* DataType */
+            code span.dv { color: #40a070; } /* DecVal */
+            code span.er { color: #ff0000; font-weight: bold; } /* Error */
+            code span.ex { } /* Extension */
+            code span.fl { color: #40a070; } /* Float */
+            code span.fu { color: #06287e; } /* Function */
+            code span.im { } /* Import */
+            code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
+            code span.kw { color: #007020; font-weight: bold; } /* Keyword */
+            code span.op { color: #666666; } /* Operator */
+            code span.ot { color: #007020; } /* Other */
+            code span.pp { color: #bc7a00; } /* Preprocessor */
+            code span.sc { color: #4070a0; } /* SpecialChar */
+            code span.ss { color: #bb6688; } /* SpecialString */
+            code span.st { color: #4070a0; } /* String */
+            code span.va { color: #19177c; } /* Variable */
+            code span.vs { color: #4070a0; } /* VerbatimString */
+            code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
+            </style>
+                                            <style>
             body {
                 font-family: Georgia;
                 max-width: 800px;
@@ -157,6 +220,7 @@ <h2>Firstname Surname</h2>
                 <li><a href="#acknowledgements">Acknowledgements</a></li>
                 <li><a href="#list-of-figures">List of figures</a></li>
                 <li><a href="#list-of-tables">List of tables</a></li>
+                <li><a href="#abbreviations">Abbreviations</a></li>
                 <li><a href="#introduction-with-a-citation"><span class="toc-section-number">1</span> Introduction, with a citation</a><ul>
                 <li><a href="#background"><span class="toc-section-number">1.1</span> Background</a></li>
                 <li><a href="#the-middle-bit"><span class="toc-section-number">1.2</span> The middle bit</a><ul>
@@ -169,10 +233,10 @@ <h2>Firstname Surname</h2>
                 <li><a href="#the-middle"><span class="toc-section-number">2.2</span> The middle</a></li>
                 <li><a href="#conclusion"><span class="toc-section-number">2.3</span> Conclusion</a></li>
                 </ul></li>
-                <li><a href="#first-research-study"><span class="toc-section-number">3</span> First research study</a><ul>
+                <li><a href="#first-research-study-with-code"><span class="toc-section-number">3</span> First research study, with code</a><ul>
                 <li><a href="#introduction-1"><span class="toc-section-number">3.1</span> Introduction</a></li>
                 <li><a href="#method"><span class="toc-section-number">3.2</span> Method</a><ul>
-                <li><a href="#subsection-1"><span class="toc-section-number">3.2.1</span> Subsection 1</a></li>
+                <li><a href="#subsection-1-with-example-code-block"><span class="toc-section-number">3.2.1</span> Subsection 1 with example code block</a></li>
                 <li><a href="#subsection-2"><span class="toc-section-number">3.2.2</span> Subsection 2</a></li>
                 </ul></li>
                 <li><a href="#results"><span class="toc-section-number">3.3</span> Results</a></li>
@@ -182,7 +246,7 @@ <h2>Firstname Surname</h2>
                 <li><a href="#research-containing-a-figure"><span class="toc-section-number">4</span> Research containing a figure</a><ul>
                 <li><a href="#introduction-2"><span class="toc-section-number">4.1</span> Introduction</a></li>
                 <li><a href="#method-1"><span class="toc-section-number">4.2</span> Method</a><ul>
-                <li><a href="#subsection-1-1"><span class="toc-section-number">4.2.1</span> Subsection 1</a></li>
+                <li><a href="#subsection-1"><span class="toc-section-number">4.2.1</span> Subsection 1</a></li>
                 <li><a href="#subsection-2-1"><span class="toc-section-number">4.2.2</span> Subsection 2</a></li>
                 </ul></li>
                 <li><a href="#results-1"><span class="toc-section-number">4.3</span> Results</a></li>
@@ -192,7 +256,7 @@ <h2>Firstname Surname</h2>
                 <li><a href="#research-containing-a-table"><span class="toc-section-number">5</span> Research containing a table</a><ul>
                 <li><a href="#introduction-3"><span class="toc-section-number">5.1</span> Introduction</a></li>
                 <li><a href="#method-2"><span class="toc-section-number">5.2</span> Method</a><ul>
-                <li><a href="#subsection-1-2"><span class="toc-section-number">5.2.1</span> Subsection 1</a></li>
+                <li><a href="#subsection-1-1"><span class="toc-section-number">5.2.1</span> Subsection 1</a></li>
                 <li><a href="#subsection-2-2"><span class="toc-section-number">5.2.2</span> Subsection 2</a></li>
                 </ul></li>
                 <li><a href="#results-2"><span class="toc-section-number">5.3</span> Results</a></li>
@@ -202,7 +266,7 @@ <h2>Firstname Surname</h2>
                 <li><a href="#final-research-study"><span class="toc-section-number">6</span> Final research study</a><ul>
                 <li><a href="#introduction-4"><span class="toc-section-number">6.1</span> Introduction</a></li>
                 <li><a href="#method-3"><span class="toc-section-number">6.2</span> Method</a><ul>
-                <li><a href="#subsection-1-3"><span class="toc-section-number">6.2.1</span> Subsection 1</a></li>
+                <li><a href="#subsection-1-2"><span class="toc-section-number">6.2.1</span> Subsection 1</a></li>
                 <li><a href="#subsection-2-3"><span class="toc-section-number">6.2.2</span> Subsection 2</a></li>
                 </ul></li>
                 <li><a href="#results-3"><span class="toc-section-number">6.3</span> Results</a></li>
@@ -215,6 +279,7 @@ <h2>Firstname Surname</h2>
                 </ul></li>
                 <li><a href="#appendix-1-some-extra-stuff">Appendix 1: Some extra stuff</a></li>
                 <li><a href="#appendix-2-some-more-extra-stuff">Appendix 2: Some more extra stuff</a></li>
+                <li><a href="#references">References</a></li>
                 </ul>
             </div>
                                 <!-- 
@@ -225,36 +290,43 @@ <h2>Firstname Surname</h2>
 
 <!-- This page is for an official declaration. -->
 
-<p> </p>
+<p>   </p>
 <h1 id="abstract" class="unnumbered">Abstract</h1>
 <!-- This is the abstract -->
 <p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nam et turpis gravida, lacinia ante sit amet, sollicitudin erat. Aliquam efficitur vehicula leo sed condimentum. Phasellus lobortis eros vitae rutrum egestas. Vestibulum ante ipsum primis in faucibus orci luctus et ultrices posuere cubilia Curae; Donec at urna imperdiet, vulputate orci eu, sollicitudin leo. Donec nec dui sagittis, malesuada erat eget, vulputate tellus. Nam ullamcorper efficitur iaculis. Mauris eu vehicula nibh. In lectus turpis, tempor at felis a, egestas fermentum massa.</p>
+
 <h1 id="acknowledgements" class="unnumbered">Acknowledgements</h1>
 <!-- This is for acknowledging all of the people who helped out -->
 <p>Interdum et malesuada fames ac ante ipsum primis in faucibus. Aliquam congue fermentum ante, semper porta nisl consectetur ut. Duis ornare sit amet dui ac faucibus. Phasellus ullamcorper leo vitae arcu ultricies cursus. Duis tristique lacus eget metus bibendum, at dapibus ante malesuada. In dictum nulla nec porta varius. Fusce et elit eget sapien fringilla maximus in sit amet dui.</p>
 <p>Mauris eget blandit nisi, faucibus imperdiet odio. Suspendisse blandit dolor sed tellus venenatis, venenatis fringilla turpis pretium. Donec pharetra arcu vitae euismod tincidunt. Morbi ut turpis volutpat, ultrices felis non, finibus justo. Proin convallis accumsan sem ac vulputate. Sed rhoncus ipsum eu urna placerat, sed rhoncus erat facilisis. Praesent vitae vestibulum dui. Proin interdum tellus ac velit varius, sed finibus turpis placerat.</p>
 <!-- Use the \newpage command to force a new page -->
 
-<p></p>
+
+
+
 <h1 id="list-of-figures" class="unnumbered">List of figures</h1>
-<!-- 
+<!--
 For me, this was the only drawback of writing in Markdown: it is not possible to add a short caption to figures and tables. This means that the \listoftables and \listoffigures commands will generate lists using the full titles, which is probably isn't what you want. For now, the solution is to create the lists manually, when everything else is finished.
 -->
-<p>Figure 4.1 This is an example figure . . . <br />
-Figure x.x Short title of the figure . . . </p>
+<p><span class="citation" data-cites="fig">(<span class="citeproc-not-found" data-reference-id="fig"><strong>???</strong></span>)</span>:</p>
+
+
 <h1 id="list-of-tables" class="unnumbered">List of tables</h1>
 <!-- 
 For me, this was the only drawback of writing in Markdown: it is not possible to add a short caption to figures and tables. This means that the \listoftables and \listoffigures commands will generate lists using the full titles, which is probably isn't what you want. For now, the solution is to create the lists manually, when everything else is finished.
 -->
 <p>Table 5.1 This is an example table . . . <br />
 Table x.x Short title of the figure . . . </p>
+<h1 id="abbreviations" class="unnumbered">Abbreviations</h1>
+
+
 <h1 id="introduction-with-a-citation"><span class="header-section-number">1</span> Introduction, with a citation</h1>
 <h2 id="background"><span class="header-section-number">1.1</span> Background</h2>
 <p>This is the introduction. Quisque finibus aliquet cursus. Integer in pellentesque tellus. Duis eu dignissim nulla, a porttitor enim. Quisque vehicula leo non ultrices finibus. Duis vehicula quis sem sit amet sollicitudin. Integer neque est, pharetra et auctor vel, iaculis interdum lectus.</p>
 <!-- 
 To include a reference, add the citation key shown in the references.bib file.
 -->
-<p>To include a citation to the text, just add the citation key shown in the references.bib file. The style of the citation is determined by the ref_format.csl file. For example, in The Living Sea you can find pictures of the Calypso <span class="citation">(Cousteau Jacques &amp; Dugan James 1963)</span>.</p>
+<p>To include a citation to the text, just add the citation key shown in the references.bib file. The style of the citation is determined by the ref_format.csl file. For example, in The Living Sea you can find pictures of the Calypso <span class="citation" data-cites="Cousteau1963">(Cousteau Jacques &amp; Dugan James 1963)</span>.</p>
 <p>In neque mauris, maximus at sapien a, iaculis dignissim justo. Aliquam erat volutpat. Praesent varius risus auctor est ultricies, sit amet consequat nisi laoreet. Suspendisse non est et mauris pharetra sagittis non porta justo. Praesent malesuada metus ut sapien sodales ornare.</p>
 <h2 id="the-middle-bit"><span class="header-section-number">1.2</span> The middle bit</h2>
 <p>This is the middle bit. Phasellus quis ex in ipsum pellentesque lobortis tincidunt sed massa. Nullam euismod sem quis dictum condimentum. Suspendisse risus metus, elementum eu congue quis, viverra ac metus. Donec non lectus at lectus euismod laoreet pharetra semper dui. Donec sed eleifend erat, vel ultrices nibh. Nam scelerisque turpis ac nunc mollis, et rutrum nisl luctus.</p>
@@ -278,10 +350,8 @@ <h1 id="literature-review-with-maths"><span class="header-section-number">2</spa
 <h2 id="introduction"><span class="header-section-number">2.1</span> Introduction</h2>
 <p>This is the introduction. Duis in neque felis. In hac habitasse platea dictumst. Cras eget rutrum elit. Pellentesque tristique venenatis pellentesque. Cras eu dignissim quam, vel sodales felis. Vestibulum efficitur justo a nibh cursus eleifend. Integer ultrices lorem at nunc efficitur lobortis.</p>
 <h2 id="the-middle"><span class="header-section-number">2.2</span> The middle</h2>
-<p>This is the literature review. Nullam quam odio, volutpat ac ornare quis, vestibulum nec nulla. Aenean nec dapibus neque. Mathematical formula can be inserted using Latex:</p>
-<ol style="list-style-type: decimal">
-<li><span class="math inline"><em>f</em>(<em>x</em>) = <em>a</em><em>x</em><sup>3</sup> + <em>b</em><em>x</em><sup>2</sup> + <em>c</em><em>x</em> + <em>d</em></span></li>
-</ol>
+<p>This is the literature review. Nullam quam odio, volutpat ac ornare quis, vestibulum nec nulla. Aenean nec dapibus in mL/min<sup>-1</sup>. Mathematical formula can be inserted using Latex and can be automatically numbered:</p>
+<p><span id="eq:my_equation" class="eqnos"><span class="math inline"><em>f</em>(<em>x</em>) = <em>a</em><em>x</em><sup>3</sup> + <em>b</em><em>x</em><sup>2</sup> + <em>c</em><em>x</em> + <em>d</em></span><span class="eqnos-number">(1)</span></span> </p>
 <p>Nunc eleifend, ex a luctus porttitor, felis ex suscipit tellus, ut sollicitudin sapien purus in libero. Nulla blandit eget urna vel tempus. Praesent fringilla dui sapien, sit amet egestas leo sollicitudin at.</p>
 <p>Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Sed faucibus pulvinar volutpat. Ut semper fringilla erat non dapibus. Nunc vitae felis eget purus placerat finibus laoreet ut nibh.</p>
 <h2 id="conclusion"><span class="header-section-number">2.3</span> Conclusion</h2>
@@ -292,13 +362,20 @@ <h2 id="conclusion"><span class="header-section-number">2.3</span> Conclusion</h
 <li>second item in the list</li>
 <li>third item in the list</li>
 </ul>
-<h1 id="first-research-study"><span class="header-section-number">3</span> First research study</h1>
+<h1 id="first-research-study-with-code"><span class="header-section-number">3</span> First research study, with code</h1>
 <h2 id="introduction-1"><span class="header-section-number">3.1</span> Introduction</h2>
 <p>This is the introduction. Nam mollis congue tortor, sit amet convallis tortor mollis eget. Fusce viverra ut magna eu sagittis. Vestibulum at ultrices sapien, at elementum urna. Nam a blandit leo, non lobortis quam. Aliquam feugiat turpis vitae tincidunt ultricies. Mauris ullamcorper pellentesque nisl, vel molestie lorem viverra at.</p>
 <h2 id="method"><span class="header-section-number">3.2</span> Method</h2>
 <p>Suspendisse iaculis in lacus ut dignissim. Cras dignissim dictum eleifend. Suspendisse potenti. Suspendisse et nisi suscipit, vestibulum est at, maximus sapien. Sed ut diam tortor.</p>
-<h3 id="subsection-1"><span class="header-section-number">3.2.1</span> Subsection 1</h3>
+<h3 id="subsection-1-with-example-code-block"><span class="header-section-number">3.2.1</span> Subsection 1 with example code block</h3>
 <p>This is the first part of the methodology. Cras porta dui a dolor tincidunt placerat. Cras scelerisque sem et malesuada vestibulum. Vivamus faucibus ligula ac sodales consectetur. Aliquam vel tristique nisl. Aliquam erat volutpat. Pellentesque iaculis enim sit amet posuere facilisis. Integer egestas quam sit amet nunc maximus, id bibendum ex blandit.</p>
+<p>For syntax highlighting in code blocks, add three “`” characters before and after a code block:</p>
+<div class="sourceCode" id="cb1"><pre class="sourceCode python"><code class="sourceCode python"><a class="sourceLine" id="cb1-1" data-line-number="1">mood <span class="op">=</span> <span class="st">&#39;happy&#39;</span></a>
+<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="cf">if</span> mood <span class="op">==</span> <span class="st">&#39;happy&#39;</span>:</a>
+<a class="sourceLine" id="cb1-3" data-line-number="3">    <span class="bu">print</span>(<span class="st">&quot;I am a happy robot&quot;</span>)</a></code></pre></div>
+Alternatively, you can also use LaTeX to create a code block as shown in the Java example below:
+
+<p>If you use <code>javaCodeStyle</code> as defined in the <code>preamble.tex</code>, it is best to keep the maximum line length in the source code at 80 characters.</p>
 <h3 id="subsection-2"><span class="header-section-number">3.2.2</span> Subsection 2</h3>
 <p>This is the second part of the methodology. Proin tincidunt odio non sem mollis tristique. Fusce pharetra accumsan volutpat. In nec mauris vel orci rutrum dapibus nec ac nibh. Praesent malesuada sagittis nulla, eget commodo mauris ultricies eget. Suspendisse iaculis finibus ligula.</p>
 <!-- 
@@ -315,7 +392,7 @@ <h2 id="introduction-2"><span class="header-section-number">4.1</span> Introduct
 <p>This is the introduction. Sed vulputate tortor at nisl blandit interdum. Cras sagittis massa ex, quis eleifend purus condimentum congue. Maecenas tristique, justo vitae efficitur mollis, mi nulla varius elit, in consequat ligula nulla ut augue. Phasellus diam sapien, placerat sit amet tempor non, lobortis tempus ante.</p>
 <h2 id="method-1"><span class="header-section-number">4.2</span> Method</h2>
 <p>Donec imperdiet, lectus vestibulum sagittis tempus, turpis dolor euismod justo, vel tempus neque libero sit amet tortor. Nam cursus commodo tincidunt.</p>
-<h3 id="subsection-1-1"><span class="header-section-number">4.2.1</span> Subsection 1</h3>
+<h3 id="subsection-1"><span class="header-section-number">4.2.1</span> Subsection 1</h3>
 <p>This is the first part of the methodology. Duis tempor sapien sed tellus ultrices blandit. Sed porta mauris tortor, eu vulputate arcu dapibus ac. Curabitur sodales at felis efficitur sollicitudin. Quisque at neque sollicitudin, mollis arcu vitae, faucibus tellus.</p>
 <h3 id="subsection-2-1"><span class="header-section-number">4.2.2</span> Subsection 2</h3>
 <p>This is the second part of the methodology. Sed ut ipsum ultrices, interdum ipsum vel, lobortis diam. Curabitur sit amet massa quis tortor molestie dapibus a at libero. Mauris mollis magna quis ante vulputate consequat. Integer leo turpis, suscipit ac venenatis pellentesque, efficitur non sem. Pellentesque eget vulputate turpis. Etiam id nibh at elit fermentum interdum.</p>
@@ -325,10 +402,22 @@ <h3 id="subsection-2-1"><span class="header-section-number">4.2.2</span> Subsect
 <h2 id="results-1"><span class="header-section-number">4.3</span> Results</h2>
 <p>These are the results. In vitae odio at libero elementum fermentum vel iaculis enim. Nullam finibus sapien in congue condimentum. Curabitur et ligula et ipsum mollis fringilla.</p>
 <h2 id="discussion-1"><span class="header-section-number">4.4</span> Discussion</h2>
-<p>Figure  shows how to add a figure. Donec ut lacinia nibh. Nam tincidunt augue et tristique cursus. Vestibulum sagittis odio nisl, a malesuada turpis blandit quis. Cras ultrices metus tempor laoreet sodales. Nam molestie ipsum ac imperdiet laoreet. Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas.</p>
-<div class="figure">
-<embed src="source/figures/example_figure.pdf" />
-<p class="caption">RV Calypso is a former British Royal Navy minesweeper converted into a research vessel for the oceanographic researcher Jacques-Yves Cousteau. It was equipped with a mobile laboratory for underwater field research. </p>
+<!--
+Figures can be either referenced using @fig:mylabel, and can be auto-completed
+to **Fig. number: mylabel**  See https://github.com/tomduck/pandoc-fignos
+-->
+<p>fig. <a href="#fig:my_fig">1</a> shows how to add a figure. Donec ut lacinia nibh. Nam tincidunt augue et tristique cursus. Vestibulum sagittis odio nisl, a malesuada turpis blandit quis. Cras ultrices metus tempor laoreet sodales. Nam molestie ipsum ac imperdiet laoreet. Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas.</p>
+<!-- 
+Figures can be added with the following syntax:
+![my_caption ](source/figures/my_image.pdf){#fig:mylabel}{ width=50% }
+
+For details on setting attributes like width and height, see:
+http://pandoc.org/MANUAL.html#extension-link_attributes
+-->
+<div id="fig:my_fig" class="fignos">
+<figure>
+<embed src="source/figures/example_figure.pdf" /><figcaption><span>Figure 1:</span> RV Calypso is a former British Royal Navy minesweeper converted into a research vessel for the oceanographic researcher Jacques-Yves Cousteau. It was equipped with a mobile laboratory for underwater field research.</figcaption>
+</figure>
 </div>
 <h2 id="conclusion-2"><span class="header-section-number">4.5</span> Conclusion</h2>
 <p>This is the conclusion to the chapter. Quisque nec purus a quam consectetur volutpat. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. In lorem justo, convallis quis lacinia eget, laoreet eu metus. Fusce blandit tellus tellus. Curabitur nec cursus odio. Quisque tristique eros nulla, vitae finibus lorem aliquam quis. Interdum et malesuada fames ac ante ipsum primis in faucibus.</p>
@@ -337,7 +426,7 @@ <h2 id="introduction-3"><span class="header-section-number">5.1</span> Introduct
 <p>This is the introduction. Phasellus non purus id mauris aliquam rutrum vitae quis tellus. Maecenas rhoncus ligula nulla, fringilla placerat mi consectetur eu. Aenean nec metus ac est ornare posuere. Nunc ipsum lacus, gravida commodo turpis quis, rutrum eleifend erat. Pellentesque id lorem eget ante porta tincidunt nec nec tellus.</p>
 <h2 id="method-2"><span class="header-section-number">5.2</span> Method</h2>
 <p>Vivamus consectetur, velit in congue lobortis, massa massa lacinia urna, sollicitudin semper ipsum augue quis tortor. Donec quis nisl at arcu volutpat ultrices. Maecenas ex nibh, consequat ac blandit sit amet, molestie in odio. Morbi finibus libero et nisl dignissim, at ultricies ligula pulvinar.</p>
-<h3 id="subsection-1-2"><span class="header-section-number">5.2.1</span> Subsection 1</h3>
+<h3 id="subsection-1-1"><span class="header-section-number">5.2.1</span> Subsection 1</h3>
 <p>This is the first part of the methodology. Integer leo erat, commodo in lacus vel, egestas varius elit. Nulla eget magna quam. Nullam sollicitudin dolor ut ipsum varius tincidunt. Duis dignissim massa in ipsum accumsan imperdiet. Maecenas suscipit sapien sed dui pharetra blandit. Morbi fermentum est vel quam pretium maximus.</p>
 <h3 id="subsection-2-2"><span class="header-section-number">5.2.2</span> Subsection 2</h3>
 <p>This is the second part of the methodology. Nullam accumsan condimentum eros eu volutpat. Maecenas quis ligula tempor, interdum ante sit amet, aliquet sem. Fusce tellus massa, blandit id tempus at, cursus in tortor. Nunc nec volutpat ante. Phasellus dignissim ut lectus quis porta. Lorem ipsum dolor sit amet, consectetur adipiscing elit.</p>
@@ -345,46 +434,49 @@ <h3 id="subsection-2-2"><span class="header-section-number">5.2.2</span> Subsect
 Comments can be added like this.
 -->
 <h2 id="results-2"><span class="header-section-number">5.3</span> Results</h2>
-<p>Table  shows us how to add a table. Integer tincidunt sed nisl eget pellentesque. Mauris eleifend, nisl non lobortis fringilla, sapien eros aliquet orci, vitae pretium massa neque eu turpis. Pellentesque tincidunt aliquet volutpat. Ut ornare dui id ex sodales laoreet.</p>
+<!-- Table formatting works same as figure formatting -->
+<p>Table <a href="#tbl:my_table">1</a> shows us how to add a table. Integer tincidunt sed nisl eget pellentesque. Mauris eleifend, nisl non lobortis fringilla, sapien eros aliquet orci, vitae pretium massa neque eu turpis. Pellentesque tincidunt aliquet volutpat. Ut ornare dui id ex sodales laoreet.</p>
 <!-- Force the table onto a newpage -->
 
-<table>
-<caption>This is the table caption. Suspendisse blandit dolor sed tellus venenatis, venenatis fringilla turpis pretium. </caption>
+<div id="tbl:my_table" class="tablenos">
+<table style="width:89%;">
+<caption><span>Table 1:</span> This is the table caption. Suspendisse blandit dolor sed tellus venenatis, venenatis fringilla turpis pretium. </caption>
 <colgroup>
-<col width="27%" />
-<col width="33%" />
-<col width="26%" />
+<col style="width: 27%" />
+<col style="width: 33%" />
+<col style="width: 27%" />
 </colgroup>
 <thead>
 <tr class="header">
-<th align="left">Column 1</th>
-<th align="left">Column 2</th>
-<th align="left">Column 3</th>
+<th style="text-align: left;">Column 1</th>
+<th style="text-align: left;">Column 2</th>
+<th style="text-align: left;">Column 3</th>
 </tr>
 </thead>
 <tbody>
 <tr class="odd">
-<td align="left">Row 1</td>
-<td align="left">0.1</td>
-<td align="left">0.2</td>
+<td style="text-align: left;">Row 1</td>
+<td style="text-align: left;">0.1</td>
+<td style="text-align: left;">0.2</td>
 </tr>
 <tr class="even">
-<td align="left">Row 2</td>
-<td align="left">0.3</td>
-<td align="left">0.3</td>
+<td style="text-align: left;">Row 2</td>
+<td style="text-align: left;">0.3</td>
+<td style="text-align: left;">0.3</td>
 </tr>
 <tr class="odd">
-<td align="left">Row 3</td>
-<td align="left">0.4</td>
-<td align="left">0.4</td>
+<td style="text-align: left;">Row 3</td>
+<td style="text-align: left;">0.4</td>
+<td style="text-align: left;">0.4</td>
 </tr>
 <tr class="even">
-<td align="left">Row 4</td>
-<td align="left">0.5</td>
-<td align="left">0.6</td>
+<td style="text-align: left;">Row 4</td>
+<td style="text-align: left;">0.5</td>
+<td style="text-align: left;">0.6</td>
 </tr>
 </tbody>
 </table>
+</div>
 <h2 id="discussion-2"><span class="header-section-number">5.4</span> Discussion</h2>
 <p>This is the discussion. Etiam sit amet mi eros. Donec vel nisi sed purus gravida fermentum at quis odio. Vestibulum quis nisl sit amet justo maximus molestie. Maecenas vitae arcu erat. Nulla facilisi. Nam pretium mauris eu enim porttitor, a mattis velit dictum. Nulla sit amet ligula non mauris volutpat fermentum quis vitae sapien.</p>
 <h2 id="conclusion-3"><span class="header-section-number">5.5</span> Conclusion</h2>
@@ -394,7 +486,7 @@ <h2 id="introduction-4"><span class="header-section-number">6.1</span> Introduct
 <p>This is the introduction. Nunc lorem odio, laoreet eu turpis at, condimentum sagittis diam. Phasellus metus ligula, auctor ac nunc vel, molestie mattis libero. Praesent id posuere ex, vel efficitur nibh. Quisque vestibulum accumsan lacus vitae mattis.</p>
 <h2 id="method-3"><span class="header-section-number">6.2</span> Method</h2>
 <p>In tincidunt viverra dolor, ac pharetra tellus faucibus eget. Pellentesque tempor a enim nec venenatis. Morbi blandit magna imperdiet posuere auctor. Maecenas in maximus est.</p>
-<h3 id="subsection-1-3"><span class="header-section-number">6.2.1</span> Subsection 1</h3>
+<h3 id="subsection-1-2"><span class="header-section-number">6.2.1</span> Subsection 1</h3>
 <p>This is the first part of the methodology. Praesent mollis sem diam, sit amet tristique lacus vulputate quis. Vivamus rhoncus est rhoncus tellus lacinia, a interdum sem egestas. Curabitur quis urna vel quam blandit semper vitae a leo. Nam vel lectus lectus.</p>
 <h3 id="subsection-2-3"><span class="header-section-number">6.2.2</span> Subsection 2</h3>
 <p>This is the second part of the methodology. Aenean vel pretium tortor. Aliquam erat volutpat. Quisque quis lobortis mi. Nulla turpis leo, ultrices nec nulla non, ullamcorper laoreet risus.</p>
@@ -427,6 +519,7 @@ <h1 id="appendix-2-some-more-extra-stuff" class="unnumbered">Appendix 2: Some mo
 This could include extra figures or raw data
 -->
 <p>Add appendix 2 here. Aliquam rhoncus mauris ac neque imperdiet, in mattis eros aliquam. Etiam sed massa et risus posuere rutrum vel et mauris. Integer id mauris sed arcu venenatis finibus. Etiam nec hendrerit purus, sed cursus nunc. Pellentesque ac luctus magna. Aenean non posuere enim, nec hendrerit lacus. Etiam lacinia facilisis tempor. Aenean dictum nunc id felis rhoncus aliquam.</p>
+
 <!-- 
 Do not edit this page.
 
@@ -434,8 +527,8 @@ <h1 id="appendix-2-some-more-extra-stuff" class="unnumbered">Appendix 2: Some mo
 
 ...which you should create using your reference manager.
 -->
-<div class="references">
 <h1 id="references" class="unnumbered">References</h1>
+<div id="refs" class="references">
 <div id="ref-Cousteau1963">
 <p>Cousteau Jacques &amp; Dugan James, 1963. <em>The Living Sea: by Jacques-Yves Cousteau</em>, London: Hamish Hamilton.</p>
 </div>
diff --git a/output/thesis.pdf b/output/thesis.pdf
index 420a702e..9284b606 100644
Binary files a/output/thesis.pdf and b/output/thesis.pdf differ
diff --git a/scratch/cleaned_tables.md b/scratch/cleaned_tables.md
new file mode 100644
index 00000000..7673b9dc
--- /dev/null
+++ b/scratch/cleaned_tables.md
@@ -0,0 +1,25 @@
+  -----------------------------------------------------------------------------------
+    Landmass     \%    Number of  Dolphins per    How Many     How Many    Forbidden
+                stuff    Owls        Capita         Foos         Bars        Float
+  ------------ ------- --------- -------------- ------------ ------------ -----------
+     North       94%    20,028       17,465        12,084       20,659       1.71
+    America                                                               
+
+    Central      91%     6564         6350         8,189        12,012       1.52
+    America                                                               
+
+     South       86%     3902         4127         5,205        6,565        1.28
+    America                                                               
+
+     Africa      84%     2892         3175         3,862        4,248         1.1
+
+     Europe      92%    20,964       17,465        15,303       24,203       1.58
+
+      Asia       87%     6852         6350         8,255        11,688       1.47
+
+    Oceania      87%     4044         4127         5,540        6,972        1.28
+
+   Antarctica    83%     2964         3175         4,402        4,941        1.13
+  -----------------------------------------------------------------------------------
+
+  Table: Important data for various land masses. {#tbl:random}
diff --git a/scratch/tables.md b/scratch/tables.md
new file mode 100644
index 00000000..cad5f63c
--- /dev/null
+++ b/scratch/tables.md
@@ -0,0 +1,12 @@
+| Landmass       | \% stuff | Number of Owls | Dolphins per Capita | How Many Foos | How Many Bars | Forbidden Float  |
+|:--------------:|:--------:|:-------------:|:--------------------:|:-----------------:|:-----------------:|:------:|
+| North America  | 94%    | 20,028      | 17,465             | 12,084          | 20,659          | 1.71 |
+| Central America  | 91%    | 6564        | 6350               | 8,189           | 12,012          | 1.52 |
+| South America  | 86%    | 3902        | 4127               | 5,205           | 6,565           | 1.28 |
+| Africa  | 84%    | 2892        | 3175               | 3,862           | 4,248           | 1.1  |
+| Europe | 92%    | 20,964      | 17,465             | 15,303          | 24,203          | 1.58 |
+| Asia | 87%    | 6852        | 6350               | 8,255           | 11,688          | 1.47 |
+| Oceania | 87%    | 4044        | 4127               | 5,540           | 6,972           | 1.28 |
+| Antarctica | 83%    | 2964        | 3175               | 4,402           | 4,941           | 1.13 |
+
+Table: Important data for various land masses. {#tbl:random}
\ No newline at end of file
diff --git a/scratch/tables.tex b/scratch/tables.tex
new file mode 100644
index 00000000..3b865761
--- /dev/null
+++ b/scratch/tables.tex
@@ -0,0 +1,161 @@
+\begin{longtable}[]{@{}ccccccc@{}}
+\caption{Important data for various land masses.
+\{\#tbl:random\}}\tabularnewline
+\toprule
+\begin{minipage}[b]{0.12\columnwidth}\centering
+Landmass\strut
+\end{minipage} & \begin{minipage}[b]{0.07\columnwidth}\centering
+\% stuff\strut
+\end{minipage} & \begin{minipage}[b]{0.09\columnwidth}\centering
+Number of Owls\strut
+\end{minipage} & \begin{minipage}[b]{0.14\columnwidth}\centering
+Dolphins per Capita\strut
+\end{minipage} & \begin{minipage}[b]{0.12\columnwidth}\centering
+How Many Foos\strut
+\end{minipage} & \begin{minipage}[b]{0.12\columnwidth}\centering
+How Many Bars\strut
+\end{minipage} & \begin{minipage}[b]{0.12\columnwidth}\centering
+Forbidden Float\strut
+\end{minipage}\tabularnewline
+\midrule
+\endfirsthead
+\toprule
+\begin{minipage}[b]{0.12\columnwidth}\centering
+Landmass\strut
+\end{minipage} & \begin{minipage}[b]{0.07\columnwidth}\centering
+\% stuff\strut
+\end{minipage} & \begin{minipage}[b]{0.09\columnwidth}\centering
+Number of Owls\strut
+\end{minipage} & \begin{minipage}[b]{0.14\columnwidth}\centering
+Dolphins per Capita\strut
+\end{minipage} & \begin{minipage}[b]{0.12\columnwidth}\centering
+How Many Foos\strut
+\end{minipage} & \begin{minipage}[b]{0.12\columnwidth}\centering
+How Many Bars\strut
+\end{minipage} & \begin{minipage}[b]{0.12\columnwidth}\centering
+Forbidden Float\strut
+\end{minipage}\tabularnewline
+\midrule
+\endhead
+\begin{minipage}[t]{0.12\columnwidth}\centering
+North America\strut
+\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\centering
+94\%\strut
+\end{minipage} & \begin{minipage}[t]{0.09\columnwidth}\centering
+20,028\strut
+\end{minipage} & \begin{minipage}[t]{0.14\columnwidth}\centering
+17,465\strut
+\end{minipage} & \begin{minipage}[t]{0.12\columnwidth}\centering
+12,084\strut
+\end{minipage} & \begin{minipage}[t]{0.12\columnwidth}\centering
+20,659\strut
+\end{minipage} & \begin{minipage}[t]{0.12\columnwidth}\centering
+1.71\strut
+\end{minipage}\tabularnewline
+\begin{minipage}[t]{0.12\columnwidth}\centering
+Central America\strut
+\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\centering
+91\%\strut
+\end{minipage} & \begin{minipage}[t]{0.09\columnwidth}\centering
+6564\strut
+\end{minipage} & \begin{minipage}[t]{0.14\columnwidth}\centering
+6350\strut
+\end{minipage} & \begin{minipage}[t]{0.12\columnwidth}\centering
+8,189\strut
+\end{minipage} & \begin{minipage}[t]{0.12\columnwidth}\centering
+12,012\strut
+\end{minipage} & \begin{minipage}[t]{0.12\columnwidth}\centering
+1.52\strut
+\end{minipage}\tabularnewline
+\begin{minipage}[t]{0.12\columnwidth}\centering
+South America\strut
+\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\centering
+86\%\strut
+\end{minipage} & \begin{minipage}[t]{0.09\columnwidth}\centering
+3902\strut
+\end{minipage} & \begin{minipage}[t]{0.14\columnwidth}\centering
+4127\strut
+\end{minipage} & \begin{minipage}[t]{0.12\columnwidth}\centering
+5,205\strut
+\end{minipage} & \begin{minipage}[t]{0.12\columnwidth}\centering
+6,565\strut
+\end{minipage} & \begin{minipage}[t]{0.12\columnwidth}\centering
+1.28\strut
+\end{minipage}\tabularnewline
+\begin{minipage}[t]{0.12\columnwidth}\centering
+Africa\strut
+\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\centering
+84\%\strut
+\end{minipage} & \begin{minipage}[t]{0.09\columnwidth}\centering
+2892\strut
+\end{minipage} & \begin{minipage}[t]{0.14\columnwidth}\centering
+3175\strut
+\end{minipage} & \begin{minipage}[t]{0.12\columnwidth}\centering
+3,862\strut
+\end{minipage} & \begin{minipage}[t]{0.12\columnwidth}\centering
+4,248\strut
+\end{minipage} & \begin{minipage}[t]{0.12\columnwidth}\centering
+1.1\strut
+\end{minipage}\tabularnewline
+\begin{minipage}[t]{0.12\columnwidth}\centering
+Europe\strut
+\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\centering
+92\%\strut
+\end{minipage} & \begin{minipage}[t]{0.09\columnwidth}\centering
+20,964\strut
+\end{minipage} & \begin{minipage}[t]{0.14\columnwidth}\centering
+17,465\strut
+\end{minipage} & \begin{minipage}[t]{0.12\columnwidth}\centering
+15,303\strut
+\end{minipage} & \begin{minipage}[t]{0.12\columnwidth}\centering
+24,203\strut
+\end{minipage} & \begin{minipage}[t]{0.12\columnwidth}\centering
+1.58\strut
+\end{minipage}\tabularnewline
+\begin{minipage}[t]{0.12\columnwidth}\centering
+Asia\strut
+\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\centering
+87\%\strut
+\end{minipage} & \begin{minipage}[t]{0.09\columnwidth}\centering
+6852\strut
+\end{minipage} & \begin{minipage}[t]{0.14\columnwidth}\centering
+6350\strut
+\end{minipage} & \begin{minipage}[t]{0.12\columnwidth}\centering
+8,255\strut
+\end{minipage} & \begin{minipage}[t]{0.12\columnwidth}\centering
+11,688\strut
+\end{minipage} & \begin{minipage}[t]{0.12\columnwidth}\centering
+1.47\strut
+\end{minipage}\tabularnewline
+\begin{minipage}[t]{0.12\columnwidth}\centering
+Oceania\strut
+\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\centering
+87\%\strut
+\end{minipage} & \begin{minipage}[t]{0.09\columnwidth}\centering
+4044\strut
+\end{minipage} & \begin{minipage}[t]{0.14\columnwidth}\centering
+4127\strut
+\end{minipage} & \begin{minipage}[t]{0.12\columnwidth}\centering
+5,540\strut
+\end{minipage} & \begin{minipage}[t]{0.12\columnwidth}\centering
+6,972\strut
+\end{minipage} & \begin{minipage}[t]{0.12\columnwidth}\centering
+1.28\strut
+\end{minipage}\tabularnewline
+\begin{minipage}[t]{0.12\columnwidth}\centering
+Antarctica\strut
+\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\centering
+83\%\strut
+\end{minipage} & \begin{minipage}[t]{0.09\columnwidth}\centering
+2964\strut
+\end{minipage} & \begin{minipage}[t]{0.14\columnwidth}\centering
+3175\strut
+\end{minipage} & \begin{minipage}[t]{0.12\columnwidth}\centering
+4,402\strut
+\end{minipage} & \begin{minipage}[t]{0.12\columnwidth}\centering
+4,941\strut
+\end{minipage} & \begin{minipage}[t]{0.12\columnwidth}\centering
+1.13\strut
+\end{minipage}\tabularnewline
+\bottomrule
+\end{longtable}
diff --git a/source/01_title_page.md b/source/01_title_page.md
index 9f43f204..3c3a90ab 100644
--- a/source/01_title_page.md
+++ b/source/01_title_page.md
@@ -9,7 +9,6 @@ and add the centred logo
 
     % Delete the following line
     % to remove the UCL header logo
-    \ThisULCornerWallPaper{1.0}{style/univ_logo.eps}
         
         \vspace*{2.5cm}
         
diff --git a/source/02_statement.md b/source/02_statement.md
index 2bc409fe..a0a46ad9 100644
--- a/source/02_statement.md
+++ b/source/02_statement.md
@@ -8,3 +8,4 @@ I, AUTHORNAME confirm that the work presented in this thesis is my own. Where in
 }
 \vspace*{\fill}
 \pagenumbering{gobble}
+\newpage
diff --git a/source/05_table_of_contents.md b/source/05_table_of_contents.md
index 2188ea4b..24090b6c 100644
--- a/source/05_table_of_contents.md
+++ b/source/05_table_of_contents.md
@@ -2,4 +2,4 @@
 
 \tableofcontents
 
-\newpage
+\newpage
\ No newline at end of file
diff --git a/source/06_list_of_figures.md b/source/06_list_of_figures.md
index f9845f3f..4f5f0ef4 100644
--- a/source/06_list_of_figures.md
+++ b/source/06_list_of_figures.md
@@ -1,13 +1,3 @@
-# List of figures {.unnumbered}
-
-<!--
-For me, this was the only drawback of writing in Markdown: it is not possible to add a short caption to figures and tables. This means that the \listoftables and \listoffigures commands will generate lists using the full titles, which is probably isn't what you want. For now, the solution is to create the lists manually, when everything else is finished.
--->
-
-Figure 4.1  This is an example figure . . .              \hfill{pp}  
-Figure x.x  Short title of the figure . . .              \hfill{pp}  
-
-\pagenumbering{roman}
-\setcounter{page}{3}
+\listoffigures
 
 \newpage
diff --git a/source/07_list_of_tables.md b/source/07_list_of_tables.md
index 04a829e1..ddaf774e 100644
--- a/source/07_list_of_tables.md
+++ b/source/07_list_of_tables.md
@@ -1,12 +1,6 @@
-# List of tables {.unnumbered}
-
-<!-- 
-For me, this was the only drawback of writing in Markdown: it is not possible to add a short caption to figures and tables. This means that the \listoftables and \listoffigures commands will generate lists using the full titles, which is probably isn't what you want. For now, the solution is to create the lists manually, when everything else is finished.
--->
-
-Table 5.1  This is an example table . . .               \hfill{pp}  
-Table x.x  Short title of the figure . . .              \hfill{pp}  
+\listoftables
 
+\newpage
 
 
 
diff --git a/source/08_abbreviations.md b/source/08_abbreviations.md
index ad746d6a..c3d4d896 100644
--- a/source/08_abbreviations.md
+++ b/source/08_abbreviations.md
@@ -6,5 +6,4 @@
 \end{tabbing}
 
 \newpage
-\setcounter{page}{1}
-\renewcommand{\thepage}{\arabic{page}}
+
diff --git a/source/09_chapter_1.md b/source/09_chapter_1.md
index 872c5560..d78df08c 100644
--- a/source/09_chapter_1.md
+++ b/source/09_chapter_1.md
@@ -1,3 +1,8 @@
+\setcounter{page}{1}
+\pagenumbering{arabic}
+\doublespacing
+\setlength{\parindent}{0.5in}
+
 # Introduction, with a citation
 
 ## Background
@@ -27,8 +32,8 @@ This is a subsection of the middle bit. Quisque sit amet tempus arcu, ac suscipi
 ## Summary of chapters
 
 <!-- 
-For italic, add one * on either side of the text
-For bold, add two * on either side of the text
+For italic, add _ on either side of the text
+For bold, add ** on either side of the text
 For bold and italic, add _** on either side of the text
 -->
 
diff --git a/source/10_chapter_2.md b/source/10_chapter_2.md
index a9c165cc..56fccb60 100644
--- a/source/10_chapter_2.md
+++ b/source/10_chapter_2.md
@@ -12,9 +12,9 @@ This is the introduction. Duis in neque felis. In hac habitasse platea dictumst.
 
 ## The middle
 
-This is the literature review. Nullam quam odio, volutpat ac ornare quis, vestibulum nec nulla. Aenean nec dapibus in mL/min^-1^. Mathematical formula can be inserted using Latex:
-
-(@ref_for_eqn1) $f(x) = ax^3 + bx^2 + cx + d$
+This is the literature review. Nullam quam odio, volutpat ac ornare quis, vestibulum nec nulla. Aenean nec dapibus in mL/min^-1^. Mathematical formula can be inserted using Latex and can be automatically numbered:
+ 
+$f(x) = ax^3 + bx^2 + cx + d$ {#eq:my_equation}
 
 Nunc eleifend, ex a luctus porttitor, felis ex suscipit tellus, ut sollicitudin sapien purus in libero. Nulla blandit eget urna vel tempus. Praesent fringilla dui sapien, sit amet egestas leo sollicitudin at.  
 
diff --git a/source/11_chapter_3.md b/source/11_chapter_3.md
index 61fddea0..c3d41ac3 100644
--- a/source/11_chapter_3.md
+++ b/source/11_chapter_3.md
@@ -20,11 +20,6 @@ if mood == 'happy':
     print("I am a happy robot")
 ```
 
-Alternatively, you can also use LaTeX to create a code block as shown in the Java example below:
-\lstinputlisting[style=javaCodeStyle, caption=Main.java]{source/code/HelloWorld.java}
-
-If you use `javaCodeStyle` as defined in the `preamble.tex`, it is best to keep the maximum line length in the source code at 80 characters.
-
 ### Subsection 2
 
 This is the second part of the methodology. Proin tincidunt odio non sem mollis tristique. Fusce pharetra accumsan volutpat. In nec mauris vel orci rutrum dapibus nec ac nibh. Praesent malesuada sagittis nulla, eget commodo mauris ultricies eget. Suspendisse iaculis finibus ligula.
diff --git a/source/12_chapter_4.md b/source/12_chapter_4.md
index 1f5305a5..8e3bc984 100644
--- a/source/12_chapter_4.md
+++ b/source/12_chapter_4.md
@@ -26,17 +26,22 @@ These are the results. In vitae odio at libero elementum fermentum vel iaculis e
 
 ## Discussion
 
-Figure \ref{ref_a_figure} shows how to add a figure. Donec ut lacinia nibh. Nam tincidunt augue et tristique cursus. Vestibulum sagittis odio nisl, a malesuada turpis blandit quis. Cras ultrices metus tempor laoreet sodales. Nam molestie ipsum ac imperdiet laoreet. Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas.
+<!--
+Figures can be either referenced using @fig:mylabel, and can be auto-completed
+to **Fig. number: mylabel** by prefixing with @ for mid-sentence references and * for the start of sentences. See https://github.com/tomduck/pandoc-fignos
+-->
+
+Fig. @fig:my_fig shows how to add a figure. Donec ut lacinia nibh. Nam tincidunt augue et tristique cursus. Vestibulum sagittis odio nisl, a malesuada turpis blandit quis. Cras ultrices metus tempor laoreet sodales. Nam molestie ipsum ac imperdiet laoreet. Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas.
 
 <!-- 
 Figures can be added with the following syntax:
-![my_caption \label{my_label}](source/figures/my_image.pdf){ width=50% }
+![main_text_caption](source/figures/my_image.pdf, "short_caption(optional)"){#fig:mylabel}{ width=50% }
 
 For details on setting attributes like width and height, see:
 http://pandoc.org/MANUAL.html#extension-link_attributes
 --> 
 
-![RV Calypso is a former British Royal Navy minesweeper converted into a research vessel for the oceanographic researcher Jacques-Yves Cousteau. It was equipped with a mobile laboratory for underwater field research. \label{ref_a_figure}](source/figures/example_figure.pdf){ width=100% }
+![RV Calypso is a former British Royal Navy minesweeper converted into a research vessel for the oceanographic researcher Jacques-Yves Cousteau. It was equipped with a mobile laboratory for underwater field research.](source/figures/example_figure.pdf "It's a boat"){#fig:my_fig width=100%}
 
 ## Conclusion
 
diff --git a/source/13_chapter_5.md b/source/13_chapter_5.md
index b9f88837..3b93f398 100644
--- a/source/13_chapter_5.md
+++ b/source/13_chapter_5.md
@@ -22,27 +22,39 @@ Comments can be added like this.
 
 ## Results
 
-Table \ref{ref_a_table} shows us how to add a table. Integer tincidunt sed nisl eget pellentesque. Mauris eleifend, nisl non lobortis fringilla, sapien eros aliquet orci, vitae pretium massa neque eu turpis. Pellentesque tincidunt aliquet volutpat. Ut ornare dui id ex sodales laoreet.
+<!-- Table formatting works same as figure formatting -->
+
+Table @tbl:random shows us how to add a table. Integer tincidunt sed nisl eget pellentesque. Mauris eleifend, nisl non lobortis fringilla, sapien eros aliquet orci, vitae pretium massa neque eu turpis. Pellentesque tincidunt aliquet volutpat. Ut ornare dui id ex sodales laoreet.
 
 <!-- Force the table onto a newpage -->
 
 \newpage
 
----------------------------------------------------------------------------
-Column 1            Column 2                Column 3
---------------      -------------------     -------------------
-Row 1               0.1                     0.2
+-----------------------------------------------------------------------------------
+Landmass      \%      Number of   Dolphins per    How Many     How Many    Forbidden
+             stuff    Owls        Capita         Foos         Bars        Float
+------------ ------- --------- -------------- ------------ ------------ -----------
+    North       94%    20,028       17,465        12,084       20,659       1.71
+ America                                                               
+
+Central      91%     6564         6350         8,189        12,012       1.52
+America                                                               
+
+    South       86%     3902         4127         5,205        6,565        1.28
+America                                                               
 
-Row 2               0.3                     0.3
+    Africa      84%     2892         3175         3,862        4,248         1.1
 
-Row 3               0.4                     0.4      
+    Europe      92%    20,964       17,465        15,303       24,203       1.58
 
-Row 4               0.5                     0.6
+    Asia       87%     6852         6350         8,255        11,688       1.47
 
----------------------------------------------------------------------------
+Oceania      87%     4044         4127         5,540        6,972        1.28
 
-Table: This is the table caption. Suspendisse blandit dolor sed tellus venenatis, venenatis fringilla turpis pretium. \label{ref_a_table}
+Antarctica    83%     2964         3175         4,402        4,941        1.13
+-----------------------------------------------------------------------------------
 
+Table: Important data for various land masses. {#tbl:random}
 
 ## Discussion
 
diff --git a/source/18_references.md b/source/18_references.md
index f556ab5a..0372f085 100644
--- a/source/18_references.md
+++ b/source/18_references.md
@@ -1,4 +1,6 @@
 \footnotesize
+\singlespacing
+\setlength{\parindent}{0in}
 
 <!-- 
 Do not edit this page.
diff --git a/style/preamble.tex b/style/preamble.tex
index ec551dbc..92cc9088 100644
--- a/style/preamble.tex
+++ b/style/preamble.tex
@@ -46,11 +46,11 @@
 \usepackage{color}
 
 % JAVA CODE BLOCKS
-\definecolor{backcolour}{RGB}{242,242,242}
-\definecolor{javared}{rgb}{0.6,0,0}
-\definecolor{javagreen}{rgb}{0.25,0.5,0.35}
-\definecolor{javapurple}{rgb}{0.5,0,0.35}
-\definecolor{javadocblue}{rgb}{0.25,0.35,0.75}
+%\definecolor{backcolour}{RGB}{242,242,242}
+%\definecolor{javared}{rgb}{0.6,0,0}
+%\definecolor{javagreen}{rgb}{0.25,0.5,0.35}
+%\definecolor{javapurple}{rgb}{0.5,0,0.35}
+%\definecolor{javadocblue}{rgb}{0.25,0.35,0.75}
 
 \lstdefinestyle{javaCodeStyle}{
   language=Java,                         % the language of the code
@@ -77,7 +77,7 @@
 %Attempt to set math size
 %First size must match the text size in the document or command will not work
 %\DeclareMathSizes{display size}{text size}{script size}{scriptscript size}.
-\DeclareMathSizes{12}{13}{7}{7}
+%\DeclareMathSizes{12}{13}{7}{7}
 
 % ---- CUSTOM AMPERSAND
 % \newcommand{\amper}{{\fontspec[Scale=.95]{Adobe Caslon Pro}\selectfont\itshape\&}}
@@ -99,14 +99,15 @@
 
 % Adjust spacing between lines to 1.5
 \usepackage{setspace}
-\onehalfspacing
-% \doublespacing
+% \onehalfspacing
+\doublespacing
 \raggedbottom
 
 % Set margins
 \usepackage[top=1.5in,bottom=1.5in,left=1.5in,right=1.4in]{geometry}
-% \setlength\parindent{0.4in} % indent at start of paragraphs (set to 0.3?)
+\setlength\parindent{0.5in} % indent at start of paragraphs (set to 0.3?)
 \setlength{\parskip}{9pt}
+\usepackage{indentfirst}
 
 % Add space between pararaphs
 % http://texblog.org/2012/11/07/correctly-typesetting-paragraphs-in-latex/
@@ -121,6 +122,7 @@
 \usepackage{booktabs}
 \usepackage{threeparttable}
 \usepackage{array}
+\usepackage{makecell}
 \newcolumntype{x}[1]{%
 >{\centering\arraybackslash}m{#1}}%
 
@@ -129,3 +131,10 @@
 
 % Don't let floats cross subsections
 % \usepackage[section,subsection]{extraplaceins}
+
+% Rotate images and tables
+\usepackage{float}
+\usepackage{pdfpages}
+\usepackage{pdflscape}
+\usepackage{graphicx}
+\usepackage{rotating}
\ No newline at end of file