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title	author	college	degree	degreedate	abstract	acknowledgements	bibliography	bibliography-heading-in-pdf	abstractseparate	bib-humanities	doi-in-bibliography	draft	page-layout	hidelinks	toc-depth	lof	lot	mini-toc	mini-lot	mini-lof	params	output	link-citations	documentclass
Flexibility in avian \ migration across scales	Benjamin Mark Van Doren	Somerville College	Doctor of Philosophy	Hilary 2020	This *R Markdown* template is for writing an Oxford University thesis. The template is built using Yihui Xie's `bookdown` package, with heavy inspiration from Chester Ismay's `thesisdown` and the `OxThesis` \LaTeX\ template (most recently adapted by John McManigle). This template's sample content include illustrations of how to write a thesis in R Markdown, and largely follows the structure from [this R Markdown workshop](https://ulyngs.github.io/rmarkdown-workshop-2019/). Congratulations for taking a step further into the lands of open, reproducible science by writing your thesis using a tool that allows you to transparently include tables and dynamically generated plots directly from the underlying data. Hip hooray!	This is where you will normally thank your advisor, colleagues, family and friends, as well as funding and institutional support. In our case, we will give our praises to the people who developed the ideas and tools that allow us to push open science a little step forward by writing plain-text, transparent, and reproducible theses in R Markdown. We must be grateful to John Gruber for inventing the original version of Markdown, to John MacFarlane for creating Pandoc (<http://pandoc.org>) which converts Markdown to a large number of output formats, and to Yihui Xie for creating `knitr` which introduced R Markdown as a way of embedding code in Markdown documents, and `bookdown` which added tools for technical and longer-form writing. Special thanks to [Chester Ismay](http://chester.rbind.io), who created the `thesisdown` package that helped many a PhD student write their theses in R Markdown. And a very special tahnks to John McManigle, whose adaption of Sam Evans' adaptation of Keith Gillow's original maths template for writing an Oxford University DPhil thesis in \LaTeX\ provided the template that I adapted for R Markdown. Finally, profuse thanks to JJ Allaire, the founder and CEO of [RStudio](http://rstudio.com), and Hadley Wickham, the mastermind of the tidyverse without whom we'd all just given up and done data science in Python instead. Thanks for making data science easier, more accessible, and more fun for us all. \begin{flushright} Ulrik Lyngs \\ Linacre College, Oxford \\ 2 December 2018 \end{flushright}	references.bib	References	true	true	true	true	twoside	true	2	true	true	true	false	false	corrections true	bookdown::pdf_book bookdown::gitbook bookdown::word_document2 template keep_tex citation_package pandoc_args templates/template.tex true biblatex --lua-filter=scripts_and_filters/correction_filter.lua css config templates/style.css sharing facebook twitter all false true false toc true	true	book

Introduction {-}

\adjustmtc

Welcome to the R Markdown Oxford University thesis template. This sample content is adapted from thesisdown and the formatting of PDF output is adapted from the OxThesis LaTeX template. Hopefully, writing your thesis in R Markdown will provide a nicer interface to the OxThesis template if you haven't used TeX or LaTeX before. More importantly, using R Markdown allows you to embed chunks of code directly into your thesis and generate plots and tables directly from the underlying data, avoiding copy-paste steps. This will get you into the habit of doing reproducible research, which benefits you long-term as a researcher, but also will greatly help anyone that is trying to reproduce or build upon your results down the road.

Using LaTeX together with Markdown is more consistent than the output of a word processor, much less prone to corruption or crashing, and the resulting file is smaller than a Word file. While you may never have had problems using Word in the past, your thesis is likely going to be about twice as large and complex as anything you've written before, taxing Word's capabilities.

Why use it? {-}

R Markdown creates a simple and straightforward way to interface with the beauty of LaTeX. Packages have been written in R to work directly with LaTeX to produce nicely formatting tables and paragraphs. In addition to creating a user friendly interface to LaTeX, R Markdown allows you to read in your data, analyze it and to visualize it using R, Python or other languages, and provide documentation and commentary on the results of your project.
Further, it allows for results of code output to be passed inline to the commentary of your results. You'll see more on this later, focusing on R. If you are more into Python or something else, you can still use R Markdown - see 'Other language engines' in Yihui Xie's R Markdown: The Definitive Guide.

Who should use it? {-}

Anyone who needs to use data analysis, math, tables, a lot of figures, complex cross-references, or who just cares about reproducibility in research can benefit from using R Markdown. If you are working in 'softer' fields, the user-friendly nature of the Markdown syntax and its ability to keep track of and easily include figures, automatically generate a table of contents, index, references, table of figures, etc. should still make it of great benefit to your thesis project.