{"id":3069,"date":"2015-11-03T10:56:15","date_gmt":"2015-11-03T18:56:15","guid":{"rendered":"http:\/\/blogs.reed.edu\/ed-tech\/?p=3069"},"modified":"2016-05-16T22:22:06","modified_gmt":"2016-05-17T05:22:06","slug":"r-markdown-senior-thesis-template","status":"publish","type":"post","link":"https:\/\/blogs.reed.edu\/ed-tech\/2015\/11\/r-markdown-senior-thesis-template\/","title":{"rendered":"R Markdown senior thesis template"},"content":{"rendered":"

\u201cScience is reportedly in the middle of a reproducibility crisis.\u201d This is the claim of quite a few these days including an article from ROpenSci<\/a> which directly references another article by The Conversation<\/a>. But what is \u201creproducible research\u201d and how can statistical tools be used to help facilitate it?<\/p>\n

<\/p>\n

\n

I agree with Roger Peng and the folks behind Coursera\u2019s massively popular Data Science Specialization and the front page of their Reproducible Research course<\/a> on their definition of \u201creproducible research\u201d:<\/p>\n

Reproducible research is the idea that data analyses, and more generally, scientific claims, are published with their data and software code so that others may verify the findings and build upon them. The need for reproducibility is increasing dramatically as data analyses become more complex, involving larger datasets and more sophisticated computations. Reproducibility allows for people to focus on the actual content of a data analysis, rather than on superficial details reported in a written summary. In addition, reproducibility makes an analysis more useful to others because the data and code that actually conducted the analysis are available.<\/p><\/blockquote>\n

One of the current goals at Reed is for students to be engaged in the research process earlier on in their academic careers in order to make their senior thesis experience more meaningful and rewarding. The collecting and analysis of data has been a challenging part of this process in the past for students. Additionally, updating statistical analyses, plots, and bibliographies as advisors request has sometimes been time consuming and frustrating.<\/p>\n

So how does this tie into the reproducible research concept? As more and more students use R Markdown<\/em> while taking courses at Reed (Chem 101\/102, Mathematics 141, Mathematics 243, and Bio 101\/102 next year!), it became clear that an option to use R Markdown<\/em> while generating the senior thesis document should be available. The simplicity of Markdown<\/em> commands improves readability and documentation, which make it a great thesis writing environment. R Markdown<\/em> provides a wonderful environment to publish data and software code along with text and commentary and, in my opinion, is the best software currently available for writing journal areedtemplates, homework assignments, AND<\/strong> senior theses\u2026.reproducible senior theses!<\/p>\n

What I\u2019ll be discussing in this blog post is a template I\u2019ve created using R Markdown<\/em> for Reed College senior theses. This template derives a lot of the features of the current LaTeX template (in fact it directly calls this template) so you can expect many of the great things from that including automatic creation of figure and table numbers, a table of contents, easy addition of beautiful plots and graphics, and the use of bibiolography style files. (Do you really want to have to memorize what APA or MLA looks like?\u2026No!) In addition, you won\u2019t need to learn LaTeX. I\u2019ve done the hard work of getting all that set up. You only need to learn Markdown<\/em>. (Don\u2019t worry. That\u2019s really not hard!)<\/p>\n

\n

Markdown<\/h3>\n

Markdown<\/em> allows you to write in an easy-to-read, easy-to-write plain text format, which then converts to a variety of different formats. R Markdown<\/em>, which is really just Markdown<\/em> with the ability to add in R<\/strong> code and output directly, allows you to produce HTML, PDF, and even Word documents based on only one Markdown<\/em> file! The sky is the limit for Markdown<\/em>!<\/p>\n

The thesis template will automatically convert the Markdown<\/em> code you type to LaTeX code which will then produce a PDF document. Again, I\u2019ve done the hard work of getting this Markdown<\/em> code to produce the correct output. If you\u2019d like to check out the current version of this PDF, it is available on Google Drive here<\/a>.<\/p>\n

Now, back to Markdown<\/em> basics. You can find a lot more information on Markdown<\/em> here<\/a> and an interactive tutorial here<\/a>. You\u2019ll get used to it before you know it. Probably in less than an hour!<\/p>\n<\/div>\n

\n

Install the template generating package<\/h3>\n

After you\u2019ve stepped through the basics of Markdown<\/em>, it\u2019s time to check out this template for yourself. Make sure you have RStudio and LaTeX installed and then direct your browser to the GitHub page for the template: http:\/\/github.com\/ismayc\/reedtemplates<\/a>. You\u2019ll see instructions there in the README.md<\/code> file near the bottom of the page on installing the template package and getting the template running. As you see there, you\u2019ll want to install the reedtemplates<\/code> package via the following commands in the RStudio console:<\/p>\n

install.packages(\"devtools\")\r\ndevtools::install_github(\"ismayc\/reedtemplates\")<\/code><\/pre>\n
This allows for Reed Senior Thesis<\/strong> to be an option when you create a new R Markdown file via the File -> New File -> R Markdown dialog. You can specify the name you would like to give the file and also the location where you\u2019d like the template and its files to be stored. I\u2019ve called it \u201cMyReedThesis\u201d in what follows. After hitting the OK button, you\u2019ll see an Rmd file load up onto your RStudio window. (It will be called the same thing as what you specified in the previous step.)<\/p>\n
If you click on the folder you\u2019ve just created in the Files tab in RStudio, you can see a lot of files that have been created to assist you. You will see Rmd files for the abstract, bibliography, different chapters, conclusion, and your main Rmd file (MyReedThesis.Rmd<\/code> for me). You also see folders that hold your bibliography database files (bib<\/code>), bibliography style files (csl<\/code>), data files (data<\/code>), and images (figure<\/code>). You\u2019ll find that I\u2019ve preloaded a bibliography database file (thesis.bib<\/code>), an American Psychological Association (APA) style file (apa.csl<\/code>) from the Zotero Style Repository<\/a>, a dataset derived from departing flights from Seattle and Portland in 2014 (flights.csv<\/code>), and a couple figures in the figure<\/code> folder.<\/p>\n
If you click on the Knit<\/strong> button near the top of the RStudio window on your main Rmd file, a PDF linking together all of the files will be created. I\u2019ve tried to show you how to do a variety of things in this Markdown<\/code> template including<\/p>\n
In the Introduction<\/strong><\/p>\n